Psyllid ID: psy3345

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------
Protein Sequence
MFNHLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL
Secondary Structure (PSIPRED)
cccccccccccccccEEcccccccccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccHHHccccHHHHHHccHHHHHHHHHcccccccccccccccccccccccccccEEEEccccccccHHHHHHHHccccccccccccccEEEEccccHHHHHHHHHccccccccEEEEEEcccccccccccccccccccHHHHHHHHHHccccHHHHHHHHcccccccEEEccccccccHHHHHHHHHHHccccEEEEcccccccccEEEEEEEEccHHHHHHHHHHHcccccccEEEEEEccccccccccccccccccccHHHHccHHHHHHHcccccHHHccccccccHHHHHHHHcccccEEEEEccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEccccccHHHHHHHHcccccccccccccccHHHHHcccHHHcccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHccccEEEEEEEccccccccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEccccccHHHHHHHHHcccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEcccccccccccEEEEEEccHHHHHHHHHHHHccccccccEEEEEEccccccHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEcccccccccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEcccccccccccHHHHHccccHHHccccccEEEEccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEEcccccccccEEEEcccHHHHHHHHHHHcccHHccccEEEcccccHHHHHHccHHHHccccEEEEEcccccccHHHHHHHHHHcccEEcccccccEEEEEcccHHHHHHHHHHccccccccEEEEEEccccHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHccHccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEccccHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEcccccEEEEcccHHHHHHHHHHHcccccccccEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHcccccccEEEEEEcccccccHHHHHHHHcccccEEEEEEEEccccccccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEccccHHHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEccccccccccEEEEEcccHHHHHHHHHHHccccEcccccEEEEEccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mfnhlsgpvvprnhislldldEVEFIYKITQEQLKAKfeekgtvtdVQLKyttegkfrrfafigyhrEDQAQAALDYFNNTYVFSSrikvekcsnlgdttkpkswskyapdssayqklhniapkqdlkpehtkdskpgkkskndptfsdflqlhgkdvskllplsnkdgeekeeenedesnnqiahadisdmEYLKLKtkskdtapsdpsvppvskapvhkrqyHTIVVknlpagvkkkdlkayfkplplasvrtTFLGMAyigfkdeknCNKALNKNKsfwkgkqlniykyskdnsakysgaaddnnnasMENIKAKHWKSQEDSVQFAEDIAESGRIFVRnlsytvtedDLTKLFEkygplaevilpidketdktkGFALVTFLMPEHATQAYQHLDGTVFLGRMlhlipgkpkenegnvdgkvhcCISERKLDAFNQVVEARSKRIIlvknlpyrtlptdlkalfepfgdlgrvlvppygiTGLVEFLQKNQAKAAFNSLaytkfkevplylewapegvfaeakekskgkekekneeegeegeeekkentaeednqqgvpeveenveedeerepepdttlyiknlnfnsTEDSIRRHFkkcgpiasvtvarkkdpkspgqflsmgyGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVkrkssnvakqtgskilvrnipfqakQSEVEELFKAFGELkfvrlpkkmvgsglhrgfgfVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNryfgtavgl
Flexible Loop (DISEMBL)
mfnhlsgpvvprnhislldLDEVEFIYKITQEQlkakfeekgtvtdvqlkyttegKFRRFAFIGYHREDQAQAALDYFNNTYVFSSrikvekcsnlgdttkpkswskyaPDSSAYQKLHniapkqdlkpehtkdskpgkkskndptFSDFLQLHGKDVSKLLPLSNKDGeekeeenedesnnqiahaDISDMEYLKLKTKskdtapsdpsvppvskapvhkrqyhtivvknlpagvkkkDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKnksfwkgkQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIpgkpkenegnvDGKVHCCISERKLDAFNQVVEARskriilvknlpyrtlPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVfaeakekskgkekekneeegeegeeekkentaeednqqgvpeveenveedeerepepdttlyiknLNFNSTEDSIRRHFKKCGpiasvtvarkkdpkspgQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIelkrsnrnleseattvkrkssnvakqtgskilvrnipfqaKQSEVEELFKAFGELKFVRLPKKmvgsglhrgfGFVEFITKNEAKRAMKALCQSTHLYGRRLVLewaeeadnvedirkrtnryfgtavgl
Low Complexity Region (SEG)
MFNHLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLsnkdgeekeeenedesnnQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFaeakekskgkekekneeegeegeeekkentaeeDNQQGvpeveenveedeerepepDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL
Disordered region (IsUnstruct)
********VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSN******************************************************************************************************************************RQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKY************************************FAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK****EGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF***********************************************************LYIKNLNFNSTEDSIRRHFKKCGPIASVTV**********QFLSMGYGFVQFYTRESLNQALKVL****************************************ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF******
Disordered Region (DISOPRED)
***************SLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCS************************************************NDPTFSDFLQLHGKDVSKLLPLSNKDGEEK**********************************************************NLPAGVKKKDLKAY*********RTTFLGMAYIGFKDEKNCNKALNKNK*FWKGKQ***************************************************RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP**************************************NLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE***********************************************************DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV***************GYGFVQFYTRESLNQALKVLQNSSLDEHQI*********************************RNIPFQAKQSEVEELFKAFGELKFVRLP******GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA***********************
Disordered Region (DISEMBL)
********VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDL****************DPTFSDFLQLHGKDVSKLLPLSN***************NQIAHADISDMEYLKLK*********************HKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKA************AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE******************************************************DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNL****************QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL
Disordered Region (DISPRO)
*FNHLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSN*****************SA**KLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNAS*E*I**KHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEE*********************************REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS***FLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTA***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFNHLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVxxxxxxxxxxxxxxxxxxxxxEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSxxxxxxxxxxxxxxxxxxxxxVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	787	2.2.26 [Sep-21-2011]
Q8R3C6	952	Probable RNA-binding prot	yes	N/A	0.437	0.361	0.511	5e-87
Q9Y4C8	960	Probable RNA-binding prot	yes	N/A	0.437	0.358	0.498	7e-85
Q6CEW9	828	Multiple RNA-binding doma	yes	N/A	0.529	0.503	0.344	2e-67
O13620	833	Multiple RNA-binding doma	yes	N/A	0.387	0.366	0.402	6e-60
Q54PB2	895	Multiple RNA-binding doma	yes	N/A	0.406	0.357	0.378	5e-58
Q6CQR6	878	Multiple RNA-binding doma	yes	N/A	0.555	0.497	0.314	9e-57
P0CR16	769	Multiple RNA-binding doma	yes	N/A	0.414	0.423	0.394	1e-56
P0CR17	769	Multiple RNA-binding doma	N/A	N/A	0.414	0.423	0.394	1e-56
Q06106	887	Multiple RNA-binding doma	yes	N/A	0.532	0.472	0.317	5e-54
Q5BGA9	819	Multiple RNA-binding doma	yes	N/A	0.385	0.369	0.381	5e-54

>sp|Q8R3C6|RBM19_MOUSE Probable RNA-binding protein 19 OS=Mus musculus GN=Rbm19 PE=1 SV=1

 Score =  322 bits (826), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 180/352 (51%), Positives = 233/352 (66%), Gaps = 8/352 (2%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           LD+F+Q    RSK +IL KNLP  TL  +++  F  FG LGRVL+P  GIT +VEFL+  
Sbjct: 571 LDSFSQAAAERSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPL 630

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGK-----EKEKNEEEGEEGEEEK 549
           +A+ AF  LAY+KF  VPLYLEWAP GVF  A +K   +     EK + E+E     E +
Sbjct: 631 EARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAEVEQETVLDPEGE 690

Query: 550 KENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 609
           K +    +   G  E EE  EE+EE E  P  TL+IKNLNF++TE++++  F K G I S
Sbjct: 691 KASVEGAEASTGKMEEEEEEEEEEEEESIPGCTLFIKNLNFSTTEETLKGVFSKVGAIKS 750

Query: 610 VTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESE 669
            T+++KK+    G  LSMG+GFV++   E   +ALK LQ  ++D H++E++ S R  +  
Sbjct: 751 CTISKKKN--KAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKP- 807

Query: 670 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 729
           A T  RK     KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 808 ALTSTRKKQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 867

Query: 730 FGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
           FGFV+FITK +AK+A  ALC STHLYGRRLVLEWA+    V+ +R++T R+F
Sbjct: 868 FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQTLRRKTARHF 919

Plays a role in embryo pre-implantation development.
Mus musculus (taxid: 10090)

>sp|Q9Y4C8|RBM19_HUMAN Probable RNA-binding protein 19 OS=Homo sapiens GN=RBM19 PE=1 SV=3

 Score =  315 bits (808), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 178/357 (49%), Positives = 232/357 (64%), Gaps = 13/357 (3%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           LD+F+Q    RSK +ILVKNLP  TL   L+  F  FG LGRVL+P  GIT +VEFL+  
Sbjct: 574 LDSFSQAAAERSKTVILVKNLPAGTLAAQLQETFGHFGSLGRVLLPEGGITAIVEFLEPL 633

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSK------GKEKEKNEEEGE---EG 545
           +A+ AF  LAY+KF  VPLYLEWAP GVF+    + K       +  EK+  E E   +G
Sbjct: 634 EARKAFRHLAYSKFHHVPLYLEWAPVGVFSSTAPQKKKLQDTPSEPMEKDPAEPETVPDG 693

Query: 546 EEEKKENTAEEDNQQGVPEVEENVEEDEEREPE-PDTTLYIKNLNFNSTEDSIRRHFKKC 604
           E  + EN  EE       ++EE  EE+EE E   P  TL+IKNLNF++TE+ ++  F K 
Sbjct: 694 ETPEDENPTEEGADNSSAKMEEEEEEEEEEEESLPGCTLFIKNLNFDTTEEKLKEVFSKV 753

Query: 605 GPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
           G + S ++++KK+    G  LSMG+GFV++   E   +ALK LQ   +D H++E++ S R
Sbjct: 754 GTVKSCSISKKKN--KAGVLLSMGFGFVEYRKPEQAQKALKQLQGHVVDGHKLEVRISER 811

Query: 665 NLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 724
             +  A T+ RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+
Sbjct: 812 ATKP-AVTLARKKQVPRKQTTSKILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGT 870

Query: 725 GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
           G HRGFGFV+F+TK +AKRA  ALC STHLYGRRLVLEWA+    ++ +R++T  +F
Sbjct: 871 GTHRGFGFVDFLTKQDAKRAFNALCHSTHLYGRRLVLEWADSEVTLQALRRKTAAHF 927

Plays a role in embryo pre-implantation development.

Homo sapiens (taxid: 9606)

>sp|Q6CEW9|MRD1_YARLI Multiple RNA-binding domain-containing protein 1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=MRD1 PE=3 SV=1

 Score =  258 bits (658), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 177/514 (34%), Positives = 262/514 (50%), Gaps = 97/514 (18%)

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           I ++GR+F+RNL YT  E+D  +LF +YG L EV LPI+ +T + KGFA V F  PE+A 
Sbjct: 297 IRKTGRLFLRNLLYTAKEEDFRQLFSQYGELEEVHLPINTKTGQCKGFAHVQFEDPENAI 356

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCIS-------ERKLDAFNQ----- 440
            AY+  DG +F GR+LH++PGKPK++   +D      +        +RK +A  Q     
Sbjct: 357 AAYEAQDGKIFQGRLLHILPGKPKKDYNRLDEHDLKNLPLKKQQELKRKAEAAKQQFSWN 416

Query: 441 --------VVEARSKRIILVKN---------------LPYRTLPTDLKALFE-------- 469
                   V+E+ +K + + K+               L   T+  D+K+ FE        
Sbjct: 417 SLYMNQDAVMESVAKSMGIKKSELIDPDSSDAAVKQALAEATVIGDVKSYFEKMGVDLAS 476

Query: 470 ----------------PFG--------------DLGRVLVPPYGITGLVEFLQKNQAKAA 499
                           PFG              DL +V++PP G   +V F     A+AA
Sbjct: 477 FDNKDRDDRVILVKNFPFGTTQPEIAEMFSEYGDLYKVMMPPAGTIAIVIFKHIPDARAA 536

Query: 500 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ 559
           F  LA+ +FK   LYLE  P+ +    K             E +E E  K++     +++
Sbjct: 537 FAKLAFRRFKTSILYLEKGPKNLLPNEK------------MESDEVEHVKQDKIVTIEDK 584

Query: 560 QGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
               +V +    D ER     T++++KNLNF +T   +   FK         V  K D K
Sbjct: 585 LSASDVMDTGSND-ERPATASTSVFVKNLNFKTTSRVLTDAFKALDGFLVAQVKMKPDSK 643

Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN 679
           + G+FLSMG+GFV+F ++E+   A K +    LD H+++LK SNR  + E T  K     
Sbjct: 644 NKGKFLSMGFGFVEFSSKEAAEIAQKAMDGHVLDGHKLQLKISNRGQDEETTETK----- 698

Query: 680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 739
             K   SKIL++N+PF+A + +V++LF AFG LK VR+PKK   +   RGF F E+++  
Sbjct: 699 --KAIDSKILIKNLPFEATKKDVQKLFGAFGSLKTVRVPKKF--NSESRGFAFAEYVSAK 754

Query: 740 EAKRAMKALCQSTHLYGRRLVLEWAE-EADNVED 772
           EA+ AM AL Q THL GRRLVL++A+ +A N E+
Sbjct: 755 EAEHAMSAL-QGTHLLGRRLVLQYAQADASNAEE 787

Involved in pre-rRNA processing.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

>sp|O13620|MRD1_SCHPO Multiple RNA-binding domain-containing protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mrd1 PE=3 SV=1

 Score =  233 bits (593), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 134/333 (40%), Positives = 195/333 (58%), Gaps = 28/333 (8%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           LDAF     ARS  ++LVKN PY T   +L +LF PFG+LGR+L+PP G   ++EFL   
Sbjct: 495 LDAFKNA--ARSDNVLLVKNFPYGTSAEELTSLFSPFGELGRILIPPAGTIAIIEFLNAP 552

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTA 554
             + AF+ LAYT+ K   LYLE AP  VF  + ++S GK            E  +K N  
Sbjct: 553 DCRQAFSKLAYTRIKSSILYLEKAPRDVFTTSFKQS-GKP-----------ELAQKVNAV 600

Query: 555 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 614
           E    + V          E+ E     T+Y+KNLNF++ ++  ++ FK      S  +  
Sbjct: 601 EATTSEKVGT--------EDIESLDTATIYVKNLNFSTKQEEFQKVFKPLEGYLSAVIRA 652

Query: 615 KKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVK 674
           K DPK PG++LSMG+GFV+F  + S   A+  +    LD H++E+K S++ +++ A   K
Sbjct: 653 KPDPKRPGKYLSMGFGFVEFKDKASAVAAMHAMNGFVLDGHKLEIKLSHQGVDAAAEVRK 712

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
           + SS   K  G+KIL++N+PF+A + +V+ L  A+G+L+ VR+PKK   S   RGF F E
Sbjct: 713 QDSS---KPKGTKILIKNLPFEATKKDVQSLLGAYGQLRSVRVPKKFDRSA--RGFAFAE 767

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEA 767
           F+T  EA  AM+AL ++THL GR LVL++A  A
Sbjct: 768 FVTAREAANAMRAL-KNTHLLGRHLVLQYASNA 799

Involved in pre-rRNA processing.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q54PB2|MRD1_DICDI Multiple RNA-binding domain-containing protein 1 OS=Dictyostelium discoideum GN=mrd1 PE=3 SV=1

 Score =  226 bits (577), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 132/349 (37%), Positives = 207/349 (59%), Gaps = 29/349 (8%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
           RS  ++LVKN+P++T   +L  LF  FG+L RV++ P     L+E++  N+AK  F +LA
Sbjct: 550 RSNTVLLVKNIPFKTQEHELHELFSKFGELSRVVLSPARTIALIEYIHPNEAKVGFKNLA 609

Query: 505 YTKFKEVPLYLEWAPEGVF---AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQG 561
           Y+KF  VPLYLEWAPEGVF   A  KE  K ++ EK+ +   + +E +            
Sbjct: 610 YSKFHHVPLYLEWAPEGVFKLPAPPKEIKKSEKSEKSSDSSNDKKEVESTTKTAATTTTT 669

Query: 562 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 621
               + N +            +YIKNLN+ +T +++   FK      +V +A K +PK+P
Sbjct: 670 KKGTDNNTQ-----------FVYIKNLNWKTTNETLVGKFKSLKDYVNVNIATKANPKNP 718

Query: 622 GQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRK----- 676
            + L  G+GF++F +++   + +K L  SS+D ++I LK S++N  +     KR+     
Sbjct: 719 SERLPCGFGFIEFSSKQGAYECIKKLNGSSIDGYEISLKLSDKNETNVQEINKRRELPEN 778

Query: 677 SSNVAKQTG-------SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 729
           S    K  G       SKI+++N+PF++   E+ +LF A+GE++ VR+PKK   +G HRG
Sbjct: 779 SKQSIKSNGGQPNKPSSKIIIKNLPFESTIKEIRKLFTAYGEIQSVRIPKK--PNGGHRG 836

Query: 730 FGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTN 778
           FGFVEF+T+ EAK AM+AL  S H YGR LVL++AE+  N++++R++ N
Sbjct: 837 FGFVEFLTEEEAKNAMEALGNS-HFYGRHLVLQYAEQDKNIDELREKAN 884

Dictyostelium discoideum (taxid: 44689)

>sp|Q6CQR6|MRD1_KLULA Multiple RNA-binding domain-containing protein 1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=MRD1 PE=3 SV=1

 Score =  222 bits (566), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 166/527 (31%), Positives = 263/527 (49%), Gaps = 90/527 (17%)

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           I E+GR+F+RN+ YT TEDD  KLF  YG L EV + +D  T ++KGFA V F   ++A 
Sbjct: 326 IRETGRLFLRNILYTATEDDFRKLFSPYGELEEVHIAVDTRTGQSKGFAYVLFKNADNAA 385

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENE--GNVDGKVHCCISERKL--------------- 435
            A+  LD  +F GR+LH++P   K++      D K      +R+L               
Sbjct: 386 TAFVELDKQIFQGRLLHILPADAKKSHKLDEFDLKNLPLKKQRELKRKANSAQQTFSWNS 445

Query: 436 -----DAF------------NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG-DLGR- 476
                DA             +++++A +    + + L   ++  D++  FE  G DL + 
Sbjct: 446 LYMNQDAVLSSVADKLGMKKSELIDAENSSSAVKQALAEASVIGDVRKFFETRGVDLTKF 505

Query: 477 ------------VLVP--PYGIT----------------------GLVEFLQKNQ---AK 497
                       +LV   PYG T                      G +  LQ      A+
Sbjct: 506 AQLKNSERDDRVILVKNFPYGTTREEIAELFLPFGKLQRLLLPPSGTIAILQFRDVPAAR 565

Query: 498 AAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEED 557
           AAF+ ++Y +FK+  +YLE  P   F    +  +  E E + ++     +E K + A+  
Sbjct: 566 AAFSKISYKRFKDGIIYLEKGPSDCFTRDAQGDELVESETDIQKAT--AKEAKISGADLL 623

Query: 558 NQQGVPEVEENVEEDEER----EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 613
             Q +P  +++  +D++     +  P  +++IKNLNF++T   +   FK         V 
Sbjct: 624 EAQSLPAADKDDHDDDDDDDDVQAGPTVSIFIKNLNFSTTSQQLTEKFKPFNGFVVAQVK 683

Query: 614 RKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTV 673
            K DPK PG+ LSMG+GF +F T+E  N  +  ++ + LD H+++LK S+R    + T+ 
Sbjct: 684 TKPDPKQPGKTLSMGFGFAEFKTKEQANAVISAMEGTILDGHKLQLKLSHR----QGTST 739

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
              SS   K+   KI+V+N+PF+A + +V ELF +FG+LK VR+PKK   S   RGF FV
Sbjct: 740 TNASSKKKKKNQGKIIVKNLPFEATRKDVFELFSSFGQLKSVRVPKKFDKSA--RGFAFV 797

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
           EF+   EA+ AM  L Q  HL GRRLV+E+ E+  + ED+ ++  + 
Sbjct: 798 EFLLPKEAENAMDQL-QGVHLLGRRLVMEFVEQ--DPEDVEQQIEKM 841

Involved in pre-rRNA processing.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

>sp|P0CR16|MRD1_CRYNJ Multiple RNA-binding domain-containing protein 1 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=MRD1 PE=3 SV=1

 Score =  222 bits (565), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 137/347 (39%), Positives = 190/347 (54%), Gaps = 21/347 (6%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
           RS+  ILVKN+PY T    L  LF P G L RVL+PP G  G+VEF     A  AF +LA
Sbjct: 414 RSQTTILVKNIPYGTSIQSLTDLFAPHGKLTRVLLPPAGTLGVVEFENHMDAGRAFKALA 473

Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE 564
           Y +     LYLE  P G+F          + E     G    E+K+E  A     + + E
Sbjct: 474 YRRLGNAVLYLEKGPVGMF----------KSETAPGVGPISTEQKREEEA-----KALAE 518

Query: 565 VEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 624
             E++ E  +   E  +TL++K LNF +T   ++         +   V  K DPK PG+ 
Sbjct: 519 KVESLPEQPDPTDEAGSTLFLKGLNFTTTTPHLQTVLSHIPGFSFARVQMKPDPKRPGEK 578

Query: 625 LSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQT 684
           LSMGYGFV F T+E+  +ALK L+   +D   +E+K + R  E +  T K   +   K  
Sbjct: 579 LSMGYGFVGFKTKEAATKALKALEGFEIDGKSLEVKFAQRGAEDDRETKKGGDAEGGKTK 638

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV----GSGLHRGFGFVEFITKNE 740
            +K+LV+N+PF+A + +V ELF A+G+LK +RLP+K V    G+   RGF F+EF T  E
Sbjct: 639 STKVLVKNLPFEATKKDVRELFSAYGQLKSLRLPRKAVPTSTGAQSTRGFAFLEFTTHTE 698

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL 787
           A RAM+AL + THL GR LVL+WA E + V DI+    +  G   G+
Sbjct: 699 AARAMEAL-KHTHLLGRHLVLQWANEGEEV-DIKGLREKVKGEVRGM 743

Involved in pre-rRNA processing.

Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (taxid: 214684)

>sp|P0CR17|MRD1_CRYNB Multiple RNA-binding domain-containing protein 1 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=MRD1 PE=3 SV=1

 Score =  222 bits (565), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 137/347 (39%), Positives = 190/347 (54%), Gaps = 21/347 (6%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
           RS+  ILVKN+PY T    L  LF P G L RVL+PP G  G+VEF     A  AF +LA
Sbjct: 414 RSQTTILVKNIPYGTSIQSLTDLFAPHGKLTRVLLPPAGTLGVVEFENHMDAGRAFKALA 473

Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE 564
           Y +     LYLE  P G+F          + E     G    E+K+E  A     + + E
Sbjct: 474 YRRLGNAVLYLEKGPVGMF----------KSETAPGVGPISTEQKREEEA-----KALAE 518

Query: 565 VEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 624
             E++ E  +   E  +TL++K LNF +T   ++         +   V  K DPK PG+ 
Sbjct: 519 KVESLPEQPDPTDEAGSTLFLKGLNFTTTTPHLQTVLSHIPGFSFARVQMKPDPKRPGEK 578

Query: 625 LSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQT 684
           LSMGYGFV F T+E+  +ALK L+   +D   +E+K + R  E +  T K   +   K  
Sbjct: 579 LSMGYGFVGFKTKEAATKALKALEGFEIDGKSLEVKFAQRGAEDDRETKKGGDAEGGKTK 638

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV----GSGLHRGFGFVEFITKNE 740
            +K+LV+N+PF+A + +V ELF A+G+LK +RLP+K V    G+   RGF F+EF T  E
Sbjct: 639 STKVLVKNLPFEATKKDVRELFSAYGQLKSLRLPRKAVPTSTGAQSTRGFAFLEFTTHTE 698

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL 787
           A RAM+AL + THL GR LVL+WA E + V DI+    +  G   G+
Sbjct: 699 AARAMEAL-KHTHLLGRHLVLQWANEGEEV-DIKGLREKVKGEVRGM 743

Involved in pre-rRNA processing.

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (taxid: 283643)

>sp|Q06106|MRD1_YEAST Multiple RNA-binding domain-containing protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MRD1 PE=1 SV=1

 Score =  213 bits (542), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 163/513 (31%), Positives = 247/513 (48%), Gaps = 94/513 (18%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           E I ++GR+F+RN+ YT  E+D  KLF  +G L EV + +D  T ++KGFA V F   ++
Sbjct: 339 EKINQTGRLFLRNILYTSKEEDFRKLFSPFGELEEVHVALDTRTGQSKGFAYVLFKDSKN 398

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKE--------------------------------- 417
           A  AY  LD  +F GR+LH++PG+ K+                                 
Sbjct: 399 AVNAYVELDKQIFQGRLLHILPGEEKKSHRLDEFDLKNMPLKKQKELKRKAAASRQTFSW 458

Query: 418 -----NEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG 472
                N+  V G V   +   K    +Q+++A +    + + L    +  D++  FE  G
Sbjct: 459 NSLYMNQDAVLGSVAAKLGLEK----SQLIDAENSSSAVKQALAEAHVIGDVRKYFESKG 514

Query: 473 -DLGR--------------VLVP--PYGIT----------------------GLVEFLQK 493
            DL +              +LV   P+G T                      G +  +Q 
Sbjct: 515 VDLTKFSQLKSTNQRDDKVILVKNFPFGTTREELGEMFLPYGKLERLLMPPAGTIAIVQF 574

Query: 494 NQAKAA---FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKK 550
               +A   F  L+Y +FK+  +YLE  P+  F +  E          +EE    E +  
Sbjct: 575 RDTTSARAAFTKLSYKRFKDGIIYLERGPKDCFTKPAEADDLINNTSAKEEENPVEVKPS 634

Query: 551 ENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV 610
            N   E N+  V E   N   DE+    P  +++IKNLNF++T  ++   FK        
Sbjct: 635 SNDLMEANKD-VTEGSSNA-HDEDVIDGPTVSIFIKNLNFSTTNQNLTDRFKVFTGFVVA 692

Query: 611 TVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA 670
            V  K DPK  G+ LSMG+GFV+F T+E  N  +  +  + +D H+I+LK S+R   S++
Sbjct: 693 QVKTKPDPKHQGKTLSMGFGFVEFRTKEQANAVIAAMDGTVIDGHKIQLKLSHRQA-SQS 751

Query: 671 TTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF 730
              K KS+   K++G KI+V+N+PF+A + +V ELF +FG+LK VR+PKK   S   RGF
Sbjct: 752 GNTKTKSN---KKSG-KIIVKNLPFEATRKDVFELFNSFGQLKSVRVPKKFDKSA--RGF 805

Query: 731 GFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW 763
            FVEF+   EA+ AM  L    HL GRRLV+++
Sbjct: 806 AFVEFLLPKEAENAMDQL-HGVHLLGRRLVMQY 837

Involved in pre-rRNA processing. Required for maintaining steady-state levels of 40S ribosomal subunit. Required for the initial processing of pre-rRNA at the A0 to A2 sites, leading to the processing of the 23S pre-rRNA intermediate to the 18S rRNA.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q5BGA9|MRD1_EMENI Multiple RNA-binding domain-containing protein 1 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=mrd1 PE=3 SV=1

 Score =  213 bits (542), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 127/333 (38%), Positives = 186/333 (55%), Gaps = 30/333 (9%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           LDAF Q    R    ILVKN  Y T   DL+ LFEPFG + R+L+PP G   +V F + +
Sbjct: 467 LDAFKQ--RERGNLAILVKNFSYGTKTEDLRKLFEPFGQITRLLMPPSGTIAIVAFARPD 524

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTA 554
           +A+ AF SLAY K  +  L+LE AP+ +F EA    +    E                  
Sbjct: 525 EAQKAFKSLAYRKLGDSILFLEKAPKDLF-EADVPPQNPLPETKAV-------------- 569

Query: 555 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 614
                QG    +    ++ + E     TL+IKNLNF++T  S+   F+      S  +  
Sbjct: 570 ----SQGFSTADTFAADEGDEEVMATATLFIKNLNFSTTNQSLIEAFRPLDGFVSARIKT 625

Query: 615 KKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVK 674
           K DPK+PGQ LSMG+GF  F T+     AL V+   +LD H + ++ S++ +++     +
Sbjct: 626 KPDPKNPGQTLSMGFGFADFKTKAQAQAALAVMNGYTLDRHTLVVRASHKGMDAAE---E 682

Query: 675 RKSSNVAKQTG---SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 731
           R+  + AK+     +KI+++N+PFQA + +V  LF A+G+L+ VR+PKK   S   RGFG
Sbjct: 683 RRKEDTAKKIAARRTKIIIKNLPFQATKKDVRSLFGAYGQLRSVRVPKKFDRSA--RGFG 740

Query: 732 FVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
           F +F++  EA+ AM AL ++THL GRRLVLE+A
Sbjct: 741 FADFVSAREAENAMDAL-KNTHLLGRRLVLEFA 772

Involved in pre-rRNA processing.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	787
14488165	849	RBD protein [Chironomus tentans]	0.911	0.844	0.394	1e-148
157104329	860	RNA binding motif protein [Aedes aegypti	0.921	0.843	0.386	1e-144
449477354	944	PREDICTED: probable RNA-binding protein	0.927	0.773	0.356	1e-129
392332679	846	PREDICTED: probable RNA-binding protein	0.881	0.820	0.359	1e-120
241147227	597	RNA binding motif protein, putative [Ixo	0.522	0.688	0.503	1e-105
321476727	845	hypothetical protein DAPPUDRAFT_306569 [	0.425	0.396	0.547	1e-101
193624932	831	PREDICTED: probable RNA-binding protein	0.414	0.392	0.540	1e-101
307180956	903	Probable RNA-binding protein 19 [Campono	0.432	0.376	0.525	7e-99
345490259	904	PREDICTED: probable RNA-binding protein	0.432	0.376	0.555	1e-98
307192625	863	Probable RNA-binding protein 19 [Harpegn	0.438	0.399	0.524	7e-98

>gi|14488165|emb|CAC42098.1| RBD protein [Chironomus tentans]

 Score =  533 bits (1373), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 332/841 (39%), Positives = 480/841 (57%), Gaps = 124/841 (14%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
           + +++L+  FE+KG VTDVQLKY  +GKFR+F FIGY  E  AQ A++YFN+T+  +S+I
Sbjct: 13  VNEQKLRKLFEQKGPVTDVQLKYK-DGKFRQFGFIGYENEGSAQEAVNYFNDTFFGTSKI 71

Query: 89  KVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKK-------S 141
           KVE C+ LGD +KPKSWSKYA DS A+ K  N   KQ  K E   +    KK        
Sbjct: 72  KVEVCAALGDESKPKSWSKYAKDSEAFIK-KNEKSKQPEKDEVEDEKSKIKKIDAIINEY 130

Query: 142 KNDPTFSDFLQLHGKDVSKLL------PLSNKDGEEKEEENEDESNNQIAHADISDMEYL 195
           K DP F +F++ H KD  KL+        +  D +E+++E E   + ++A+ +ISD EY+
Sbjct: 131 KEDPEFQEFMKSHAKD--KLIWENDVNTGTKVDQDEQKDEEESGDDTKLANQEISDAEYM 188

Query: 196 KLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRT 255
           K    + D   S        K   +  + +TI V+N+P  +K+++LK +F+P    SVR 
Sbjct: 189 KKLMGTSDETES----ISFEKKTKNLIKLYTIKVRNIPKKLKREELKKFFRPSKAHSVRI 244

Query: 256 -TFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMEN 314
                  Y+GFK E++  +AL+K+KSF KGKQ+++Y+++         ++  N+      
Sbjct: 245 PKNSNFGYVGFKLERDMKRALSKDKSFLKGKQIHVYEFTHQKEESEVKSSKINS------ 298

Query: 315 IKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET 374
                W+ QE+ ++  EDI ESG++F RNL YTVTEDD+  +FEKYG + EV +PID  T
Sbjct: 299 ----RWQEQEEKLKGEEDICESGKLFFRNLPYTVTEDDVQTVFEKYGNVVEVNVPIDPTT 354

Query: 375 DKTKGFALVTFLMPEHATQAYQHLDG---------------------------------- 400
            K KGF  VTFLMPE+A QAY  L+G                                  
Sbjct: 355 RKIKGFGTVTFLMPENAVQAYNELNGTMFHGRMFHLLPGKSNDKTEADESDPKNFKDKRR 414

Query: 401 --------------TVFLG-----RMLHLIPGKPKE-----NEGNVDGKVHCCISER--- 433
                         T+F+G      ++  + GK KE     + G     V   + E    
Sbjct: 415 KELKKTASSAHNWNTLFMGTNAVAEIISKVYGKSKEEVLESSTGGSGAAVRLALGETQAV 474

Query: 434 ------------KLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP 481
                       +L++F+     RSK IILVKNLP  T   ++K+ FE FG L +V++PP
Sbjct: 475 LDMKTFLEKHGVRLESFDDQKVKRSKTIILVKNLPANTDVEEMKSKFEQFGVLDKVVLPP 534

Query: 482 YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEE 541
             +T L++F   ++A+ AF  LAY+KFK VPLYLEWAPE VF           ++K+E+ 
Sbjct: 535 NSVTCLIKFADPSEARKAFKKLAYSKFKHVPLYLEWAPENVF-----------RDKDEDI 583

Query: 542 GEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF 601
            E   E K+E+   ED  +   EV+++        PEP+TTL+IKNLN ++ E++IR  F
Sbjct: 584 EENVNEAKEESAQNEDKNKEEEEVDDSA-------PEPNTTLFIKNLNKDTVEETIREIF 636

Query: 602 KKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKR 661
           K  G I S+ +A+KK      + + +GYGF+QF    + ++ALK +Q+  +D  +IELKR
Sbjct: 637 KNIGTIRSIQIAKKKSTDDEKKLIPLGYGFIQFKQASAADKALKTMQHKEIDGIKIELKR 696

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
           S+R L + A   ++K+ N  ++  +KI+VRNIPFQA  +E+ +LF+ FGELK VRLPKK 
Sbjct: 697 SDRTLNTPAHVSRKKTDNKKQEGSTKIMVRNIPFQANANEIRQLFQVFGELKAVRLPKK- 755

Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
            G   HRGFGF++F+TK++AK A  AL  STHLYGRRLVLEWA   ++V +IRKRT +  
Sbjct: 756 PGIDQHRGFGFIDFVTKSDAKSAFDALHHSTHLYGRRLVLEWAATEEDVTEIRKRTAKDV 815

Query: 782 G 782
           G
Sbjct: 816 G 816

Source: Chironomus tentans

Species: Chironomus tentans

Genus: Chironomus

Family: Chironomidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157104329|ref|XP_001648356.1| RNA binding motif protein [Aedes aegypti] gi|108880340|gb|EAT44565.1| AAEL004075-PA [Aedes aegypti]

 Score =  517 bits (1332), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 326/843 (38%), Positives = 460/843 (54%), Gaps = 118/843 (13%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
           IT+ +L+  F + G VTD+QLKYT EGKFR F FIGY  EDQA  A+ +FNNT++ +S+I
Sbjct: 13  ITESKLRDHFSQCGIVTDIQLKYTPEGKFRNFGFIGYETEDQASKAISHFNNTFLRTSKI 72

Query: 89  KVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPG---KKSKNDP 145
            V  C+ L +    K WSKY+      + L        +KP   K        +K KNDP
Sbjct: 73  SVAPCAALNEAKSLKVWSKYSKSKQDVKDLQKQLEDVTVKPIKKKGETAEDILQKHKNDP 132

Query: 146 TFSDFLQLHGKDVSKLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTA 205
            F +F+Q+  K  + +      D + ++ ++E   +         +   +K         
Sbjct: 133 LFKEFVQVQNKAGTAVW-----DNQLQQTDSEGSGSEDEPEEQEPEKSEIK--------- 178

Query: 206 PSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRT--TFLGMAYI 263
             +PSV    K  +       + + N+P+  K++DL  +FKP+   S+R      G AY+
Sbjct: 179 -KEPSVD--KKKELKVANLFVVKIHNIPSKTKRQDLLRFFKPVKPYSIRIPPKQKGFAYV 235

Query: 264 GFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQ 323
           G+K E    KAL K+KSF  GKQ+ +  ++  +  +     + +  +  EN K   W  Q
Sbjct: 236 GYKTEGELKKALLKDKSFLGGKQVKVVDFTAKD--RLRSEEEKSQLSKKENPK---WIRQ 290

Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
           ++SV  +E I E+G++F RNL+Y+V EDDL +LFEKYGP+AE+ LPID  T K KGF +V
Sbjct: 291 KESV-CSESIIETGKLFFRNLAYSVKEDDLKQLFEKYGPVAEIDLPIDSNTRKLKGFGMV 349

Query: 384 TFLM------------------------PEHATQAYQHLD-------------------- 399
           TFLM                        P    +  Q +D                    
Sbjct: 350 TFLMPEHAVQAYSELNGTFFHGRMFHLLPAKIDETKQEVDEDDASLNFKQKKELKLKKTA 409

Query: 400 ------GTVFLGR--MLHLIP---GKPKE----NEGNVDGKVHCCISERK---------- 434
                  T+F+G   +  ++    GK KE     EG     V   + E +          
Sbjct: 410 QSSHNWNTLFMGENAIAEVVAKKYGKTKEEVLSTEGTTSAAVRLALGETEIVSEMRQFLV 469

Query: 435 -----LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVE 489
                LDAFN V +ARS   I+ KNLP  T   +LK  F+ FG LGRV++PP G++ ++E
Sbjct: 470 DNGIHLDAFNGVPKARSNTTIIAKNLPAATELNELKERFDKFGLLGRVILPPSGVSAVIE 529

Query: 490 FLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE----AKEKSKGKEKEKNEEEGEEG 545
           FL  ++AK AF  LAY++FK +PLYLEWAPE +FA+     KE ++G+  +  + +    
Sbjct: 530 FLDPSEAKKAFKKLAYSRFKSLPLYLEWAPENIFAKPNTSVKEDTEGESTKIKKPKAPPK 589

Query: 546 EEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCG 605
           +E+       E  +     VE   +E  +  PE  TTL++KNL+F + E+SIR  F+  G
Sbjct: 590 DEQ-------ELKEPMPEPVEPEKDEYSDLSPEEGTTLFLKNLSFQTNEESIRETFRNMG 642

Query: 606 PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
           PI SV V R+KD    G+  S GYGF+QF  R+S + ALK LQ+  +D  ++EL RS+R 
Sbjct: 643 PIHSVQVVRRKDG---GKNESRGYGFIQFKLRKSADSALKNLQSVHIDGRKVELSRSDRT 699

Query: 666 LESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 725
           L +EA T  RK+S + KQTG+KILVRN+PFQA   E+ +LFK FGELK VRLP+KMV S 
Sbjct: 700 LNTEADTHGRKASKLKKQTGTKILVRNVPFQANAKEIRDLFKVFGELKSVRLPRKMVSSA 759

Query: 726 --LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGT 783
              HRGF FV+F+T+N+AK+A +ALCQSTHLYGRRLVLEWAE  D VE++RKRT   F  
Sbjct: 760 DESHRGFCFVDFVTENDAKQAFEALCQSTHLYGRRLVLEWAEADDGVEELRKRTAEKFAG 819

Query: 784 AVG 786
             G
Sbjct: 820 TSG 822

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|449477354|ref|XP_002196178.2| PREDICTED: probable RNA-binding protein 19 [Taeniopygia guttata]

 Score =  469 bits (1208), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 329/924 (35%), Positives = 465/924 (50%), Gaps = 194/924 (20%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
           + +E+ +  F   GT+TD  LKYT +G+FR+F FIGY  ED+AQAAL++FN +++ +SR+
Sbjct: 13  MKEERFRKLFAAFGTLTDCCLKYTKDGRFRKFGFIGYKSEDEAQAALNHFNKSFIDTSRL 72

Query: 89  KVEKCSNLGDTTKPKSWSKYAPDSSAYQK-----LHNIAPKQDLKPEHTKDSKPG-KKSK 142
            VE C + GD TKPK+WSK++  + A +K     L + AP    K +  KD+    K+ K
Sbjct: 73  TVELCKSFGDPTKPKAWSKHSQKAPASEKQTKEPLASAAPAGTKKGKKKKDAVDNLKELK 132

Query: 143 NDPTFSDFLQLHGKDV------------------SKLLPLSNKDGEEKEE--ENEDESNN 182
            D TF +FL +H K                    S      N D +E EE  E  DE + 
Sbjct: 133 EDKTFQEFLVVHQKRSQVATWANDTLAEEPKKGKSSAADYLNFDSDESEELSEGGDEPSE 192

Query: 183 Q-------------IAHADISDMEYLKLK---------------------------TKSK 202
                             D+SDM+YLK K                           +   
Sbjct: 193 DEEEIKGKKEGKKAATSKDLSDMDYLKSKVVKDSSSSSSTEEETETEEEESETEEDSGIA 252

Query: 203 DTAPSDPSVPPVS----KAPVHKRQYH-----------------TIVVKNLPAGVKKKDL 241
           +T P     P       K P  K++                   T+ ++  P+ + ++ +
Sbjct: 253 ETPPEKRGKPKAQQTEQKTPAGKKKKRSTLEVHQASPGEASTAFTVKLRGAPSSITEEKI 312

Query: 242 KAYFKPLPLASVRT------TFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKD 295
           + +F PL   ++R          G  ++  K E    +AL + K F  G+ + + +    
Sbjct: 313 REFFFPLKPVAIRMGKKAQGKNSGYIFVDLKSEAEMQRALKRKKEFLGGRCVEVSRC--- 369

Query: 296 NSAKYSGAADDNNNASMENIKAKH----WKSQEDSVQFAEDIAESGRIFVRNLSYTVTED 351
                        N   E + AK     W+      +  ED++ESGR+FVRNL +T TE+
Sbjct: 370 ------------RNTPKEPVPAKPEHQPWQRTLRDDEEEEDLSESGRLFVRNLPFTSTEE 417

Query: 352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLI 411
           DL K+F KYGPL+E+  PIDK T K KGFA +T+++PEHA +A   LDG VF GRM+HL+
Sbjct: 418 DLEKIFSKYGPLSEIHFPIDKLTKKPKGFAFITYMIPEHAVKALAELDGQVFQGRMMHLL 477

Query: 412 PG---KPKENEGNVD------------------------------GKVHCCISERKLDAF 438
           P    K K  +G+ +                                V   ++++   A 
Sbjct: 478 PSTIRKEKIEDGDAEESSSYKKSKEAKDKANSASSHNWNALFVGTNAVADAMAQKYNAAK 537

Query: 439 NQVVEARSK------------------RIILVKN------------------LPYRTLPT 462
           +QV++A SK                  R  LV+N                  +  + LP 
Sbjct: 538 SQVLDAESKDSVAVRVALGETELVQEIRRFLVENGVSLDSFSQAAGERSKTVILVKNLPA 597

Query: 463 DLKA-----LFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW 517
              A     LF   G LGRVL+P  GIT +VEFL+  +AK AF  LAY+KF  VPLYLEW
Sbjct: 598 GTSALELEQLFGHHGGLGRVLLPEGGITAIVEFLEPTEAKQAFTRLAYSKFHSVPLYLEW 657

Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP 577
           AP GVF      S   +K+K    G+E E       A +D+++   + EE  EE+EE E 
Sbjct: 658 APMGVFL-----SPAPQKKKAGVPGKEDEAGLVPGEATKDSEEAAAQEEEEEEEEEEEEN 712

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
            P  TL+IKNLNF +TED+++  F K G + S T+++KKD    G  LSMG+GFV++   
Sbjct: 713 IPGCTLFIKNLNFATTEDTLKETFSKVGALKSCTISKKKD--KAGTLLSMGFGFVEYKKP 770

Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA 697
           ES  +AL+ LQ  ++D H++E+K S R +   A    RK     KQ  SKILVRNIPFQA
Sbjct: 771 ESAQKALRQLQGCTVDGHKLEVKLSERAVRP-AVKSTRKKQIAKKQKTSKILVRNIPFQA 829

Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR 757
              E+ ELF  FGELK VRLPKKM G+G HRGFGFV+F+TK +AK+A +ALC STHLYGR
Sbjct: 830 TVREIRELFSTFGELKTVRLPKKMAGTGSHRGFGFVDFVTKQDAKKAFQALCHSTHLYGR 889

Query: 758 RLVLEWAEEADNVEDIRKRTNRYF 781
           RLVLEWA+  + +E +R++T ++F
Sbjct: 890 RLVLEWADTEETLEALRRKTAQHF 913

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|392332679|ref|XP_003752658.1| PREDICTED: probable RNA-binding protein 19 [Rattus norvegicus]

 Score =  439 bits (1129), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 309/860 (35%), Positives = 443/860 (51%), Gaps = 166/860 (19%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
           + +++ +  F   GT+TD  LK+T EGKFR+F FIG+  E++AQAAL++F+ +++ +SRI
Sbjct: 13  MKEDRFRQLFAAFGTLTDCSLKFTKEGKFRKFGFIGFKSEEEAQAALNHFHRSFIDTSRI 72

Query: 89  KVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPG-------KKS 141
            VE C + GD +KP++WSK+A   S  ++     P QD  P  TK  K         +K 
Sbjct: 73  TVEFCKSFGDPSKPRAWSKHAQKPSQPKQ-----PSQDSIPSDTKKDKKKKKVPSDLEKL 127

Query: 142 KNDPTFSDFLQLHGKDV----------------SKLLPL---------SNKD-GEEKEEE 175
           K D  F +FL +H K                  +K  P          SN D G+E EEE
Sbjct: 128 KEDAEFQEFLSIHQKRTQVATWANDALEAELPKAKAKPSSDYLNFDSDSNSDSGQESEEE 187

Query: 176 -----NEDESNNQIAHA---DISDMEYLKLKTKSKDT----------------------- 204
                 E+E   Q   A   ++SDM+YLK K    +                        
Sbjct: 188 PAGEDGEEEQGLQPKAAVQKELSDMDYLKSKMVRAEVSSEDEDKEDSEDEAVNCEEGSEA 247

Query: 205 -----APSDP-------------SVPPVSKA-----PVHKRQYHT---IVVKNLPAGVKK 238
                +P+ P             S+ P   A     P  +++  T   + ++  P  V +
Sbjct: 248 EEEEGSPTCPAQQAGVNRGAVLGSLRPQEAAGKVEKPASQKEPTTPYTVKLRGAPFNVTE 307

Query: 239 KDLKAYFKPLPLASVRTTF------LGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKY 292
           K++  +  PL   ++R          G  ++    E+   KAL  N+ +  G+ + +++ 
Sbjct: 308 KNVLEFLAPLKPVAIRIVRNAHGNKTGYVFVDLSSEEEVKKALKCNREYMGGRYIEVFRE 367

Query: 293 SKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDD 352
            + ++A+  GA   ++         +H +         ED+A+SGR+FVRNLSYT +E+D
Sbjct: 368 KQASAAR--GAPKSSSAPWQGRTLGEHEEE--------EDLADSGRLFVRNLSYTSSEED 417

Query: 353 LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP 412
           L KLF  YG     +        +TKG   V   + E  TQ  Q +    FL        
Sbjct: 418 LEKLFSAYGTCGLRL--------ETKGSVAVRMALGE--TQLVQEVRS--FL-------- 457

Query: 413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG 472
                    +D  V C      LD+F+Q    RSK +IL KNLP  TL  +L+ +F  FG
Sbjct: 458 ---------IDNGV-C------LDSFSQAAAERSKTVILAKNLPAGTLAAELQEIFSRFG 501

Query: 473 DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKG 532
            LGRVL+P  GIT +VEFL+  +A+ AF  LAY+KF  VPLYLEWAP GVF  A +K   
Sbjct: 502 SLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQK--- 558

Query: 533 KEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEE-----------NVEEDEEREPEPDT 581
             K+   E+  +  E ++E     + ++ + E  E             EE+EE E  P  
Sbjct: 559 --KDSQPEQPAQKAEAEQETVLNPEGEKALVEGAEASMGKMEEEEEEEEEEEEEESIPGC 616

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL+IKNLNFN+TE++++  F + G + S T+++KK     G  LSMG+GFV++   E   
Sbjct: 617 TLFIKNLNFNTTEETLKEVFSRVGAVKSCTISKKKS--KAGVLLSMGFGFVEYKKPEQAQ 674

Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
           +ALK LQ   +D H++E++ S R  +  A T  RK     KQT SKILVRNIPFQA Q E
Sbjct: 675 KALKRLQGHIVDGHKLEVRISERATKP-ALTSTRKKQVPKKQTTSKILVRNIPFQANQRE 733

Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
           + ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +AK+A  ALC STHLYGRRLVL
Sbjct: 734 IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL 793

Query: 762 EWAEEADNVEDIRKRTNRYF 781
           EWA+    V+ +R++T ++F
Sbjct: 794 EWADSEVTVQALRRKTAKHF 813

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|241147227|ref|XP_002405304.1| RNA binding motif protein, putative [Ixodes scapularis] gi|215493703|gb|EEC03344.1| RNA binding motif protein, putative [Ixodes scapularis]

 Score =  390 bits (1001), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 214/425 (50%), Positives = 289/425 (68%), Gaps = 14/425 (3%)

Query: 361 GPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEG 420
           GP++EV L IDK T K KGFA V+F+ PEHA +A+  LDG + L  M   +  +    E 
Sbjct: 179 GPISEVHLSIDKITRKPKGFAFVSFMFPEHAIKAFSELDGKL-LQEMGDSVAVRMALGET 237

Query: 421 NVDGKVHCCISER--KLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVL 478
            V  +    +  +  +LDAF +    RSK +ILVKNLP +T P +++  F  FG L RV+
Sbjct: 238 QVVTETKEFLQGQGVELDAFCRPATERSKTVILVKNLPAKTHPDEIRDAFAKFGTLSRVV 297

Query: 479 VPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKN 538
           +PP+GI  LVEF + ++A+ AF  LAY+KFK VPLYLEWAP GVF E K   K   K+  
Sbjct: 298 LPPWGICALVEFQEPSEARTAFRRLAYSKFKHVPLYLEWAPVGVFKEKKTIPKPTLKDVT 357

Query: 539 EEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIR 598
           +EE  +         +E+  ++      +  EE+EE  PEPDTTL++KNLNF++TE+++R
Sbjct: 358 KEEPTKA--------SEDGEKEAEKAERQEEEEEEEEPPEPDTTLFVKNLNFSTTEEALR 409

Query: 599 RHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE 658
            HF  CGPI  VT+A+KKD K+PG+ LSMGYGFVQF  ++S  +ALK LQ+S LDEH +E
Sbjct: 410 EHFAGCGPIHEVTIAKKKDLKNPGKMLSMGYGFVQFKLKQSAKKALKQLQHSKLDEHAVE 469

Query: 659 LKRSNR-NLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRL 717
           LK S R   +  A  +KRK +++ K++ +KILVRNIPF+A + E++ELF  FG L+ +RL
Sbjct: 470 LKLSKRETAQQTAAELKRKKTDLGKES-TKILVRNIPFEATKKELQELFSVFGTLRDIRL 528

Query: 718 PKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN-VEDIRKR 776
           PKKM G+G HRGF FV+F+TKN+AKRA +ALCQSTHLYGRRLVLEWA   D  V+ +RK+
Sbjct: 529 PKKMAGTGRHRGFAFVDFLTKNDAKRAFQALCQSTHLYGRRLVLEWASSDDQEVDTLRKK 588

Query: 777 TNRYF 781
           T  +F
Sbjct: 589 TADHF 593

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321476727|gb|EFX87687.1| hypothetical protein DAPPUDRAFT_306569 [Daphnia pulex]

 Score =  376 bits (965), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 191/349 (54%), Positives = 249/349 (71%), Gaps = 14/349 (4%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           LDAF    + RSK ++LVKNL  ++   +L+ LF PFG+LGRVL+PP G+T +VEFL+  
Sbjct: 487 LDAFQDAPKQRSKTVMLVKNLDAQSNVDELRDLFSPFGELGRVLLPPRGVTAIVEFLEPT 546

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTA 554
           +AKAAF  LAY+KF+ +PLYLEWAP  VF  A ++ + K  E   +     ++     T 
Sbjct: 547 EAKAAFRKLAYSKFRHMPLYLEWAPMDVFRTAAQRVESKPSENKTKV----KDASAVATL 602

Query: 555 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 614
           EE+N    P + + VEE    +PE DTT+++KN+NF +T+ S+R+HF+ CGPI S TVAR
Sbjct: 603 EENN----PILSDKVEE----QPEQDTTIFVKNVNFATTDQSMRKHFESCGPIFSATVAR 654

Query: 615 KKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVK 674
           KKDPK+PGQFLSMGYGFVQF ++++   ALK LQNS+LD H IELKRSNR    E T + 
Sbjct: 655 KKDPKNPGQFLSMGYGFVQFLSKKATVTALKELQNSTLDGHTIELKRSNRTENKEETIIT 714

Query: 675 -RKSSNVAKQ-TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
            RK+ + +K+   SK+LVRNIPF+A   EV ELFK FGELK VRLPKKM G+  HRGF F
Sbjct: 715 ARKTLSTSKEPISSKLLVRNIPFEATTKEVTELFKPFGELKAVRLPKKMAGNQSHRGFAF 774

Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
           ++FITK +AKRA ++L  STHLYGRRLVLEWA   D VED+R+RT  ++
Sbjct: 775 IDFITKQDAKRAFESLSASTHLYGRRLVLEWAASEDTVEDVRRRTTSHY 823

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193624932|ref|XP_001949363.1| PREDICTED: probable RNA-binding protein 19-like [Acyrthosiphon pisum]

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 192/355 (54%), Positives = 245/355 (69%), Gaps = 29/355 (8%)

Query: 423 DGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY 482
           D K++      KLD FNQ V  RSK +ILVKNLP  T   +LK +F  +G + RV++PP 
Sbjct: 477 DTKIYLENQGVKLDIFNQTVINRSKNVILVKNLPADTTELELKDIFSKYGLVNRVVLPPS 536

Query: 483 GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEG 542
           G+TGL+EF+Q ++AK AF  LAY+KFK +PLYLEWAP+ V  +                 
Sbjct: 537 GVTGLIEFVQNSEAKTAFRQLAYSKFKHLPLYLEWAPDKVLTDV---------------- 580

Query: 543 EEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK 602
                   +N  EE      P       ED+  EPE DTTL+IKN+NFN+TE+ I +HF+
Sbjct: 581 -------PQNIHEE----TFPSYTNKDTEDDIDEPESDTTLFIKNINFNTTEEHITKHFE 629

Query: 603 KCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRS 662
            CG IA+VTVARKKDP  PG+FLSMGYGF+QFY ++S+N+ALK  Q S LD H IELKRS
Sbjct: 630 PCGKIANVTVARKKDPNLPGKFLSMGYGFIQFYRQKSVNEALKTKQLSMLDNHSIELKRS 689

Query: 663 NRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV 722
           NR L+S AT  +RK     +++ +KILVRNIPFQA   EV ELFK FGELK +R+PKKMV
Sbjct: 690 NRTLQS-ATVAERKQGKSYEES-TKILVRNIPFQASIQEVIELFKTFGELKGLRMPKKMV 747

Query: 723 GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRT 777
           G+G HRGF FVE+ +K EAK AM+++CQSTHLYGRRLVLEWA+  +N++++RKRT
Sbjct: 748 GTGTHRGFAFVEYNSKTEAKAAMESMCQSTHLYGRRLVLEWAQAGENLDEMRKRT 802

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307180956|gb|EFN68744.1| Probable RNA-binding protein 19 [Camponotus floridanus]

 Score =  368 bits (944), Expect = 7e-99,   Method: Compositional matrix adjust.
 Identities = 184/350 (52%), Positives = 253/350 (72%), Gaps = 10/350 (2%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           L+AFNQ  + RS  IIL+KNLP +T  ++++ +F   G+L R+++PP GIT LVEFL+ +
Sbjct: 533 LNAFNQAPKKRSTTIILIKNLPAQTKSSEIREMFAKHGELARIVMPPAGITALVEFLEPS 592

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKS---KGKEKEKNEEEGEEGEEEKKE 551
           +A+ AF++LAY K+K +PLYLEWAP+  F     K+   K K +E+  +E  + +E KKE
Sbjct: 593 EARKAFHALAYKKYKHLPLYLEWAPDNSFTRPASKTDMIKSKSRER-RKESTDSKEAKKE 651

Query: 552 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 611
              EE  +      + + +ED+E  PEPDTTL++KN+NF++TE+ ++ +F KCGP+  +T
Sbjct: 652 IITEESKENE----KMHTKEDDE-PPEPDTTLFVKNINFSTTEEQLKDYFGKCGPLHYIT 706

Query: 612 VARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEAT 671
           +A KKDP++P   LSMGYGFV++  +   ++ALK LQ S LD   +ELKRS R L S+  
Sbjct: 707 IATKKDPENPTNKLSMGYGFVRYKRKHDADRALKTLQMSVLDGKSLELKRSERTLMSDVK 766

Query: 672 TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 731
           TV RK S V +QT SKILVRNIPFQA   E+ ELFK++GELK VRLPKK+VG+  HRGFG
Sbjct: 767 TV-RKKSKVTEQTSSKILVRNIPFQATLQEITELFKSYGELKAVRLPKKLVGTEKHRGFG 825

Query: 732 FVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
           F+E+ TK +AK+A KALCQSTHLYGRRLVLEWA+  + +E+IRKRT + F
Sbjct: 826 FIEYYTKTDAKKAFKALCQSTHLYGRRLVLEWAQAEEGIEEIRKRTAKRF 875

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345490259|ref|XP_001605134.2| PREDICTED: probable RNA-binding protein 19-like [Nasonia vitripennis]

 Score =  367 bits (942), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 196/353 (55%), Positives = 256/353 (72%), Gaps = 13/353 (3%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           L+AFNQ  +ARSK +ILVKNLP  T   +++ +F   G+LGRV++PP GIT LVEF++ +
Sbjct: 531 LNAFNQAPKARSKTVILVKNLPAGTHIREIREMFAKHGELGRVVLPPSGITALVEFIEPS 590

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKS-KGK-----EKEKNEEEGEEGEEE 548
           +A+ AF  LAY+KFK +PLYLEWAP+  F  A  KS KGK     EK +N  +G      
Sbjct: 591 EARKAFMRLAYSKFKHLPLYLEWAPDDSFTSAPPKSAKGKTDTADEKVRNNTKGNGAV-- 648

Query: 549 KKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA 608
           K E   +  N     E +E+ +E++E EPEPDTTL++KNL+F +TE+ +R+HF KCG + 
Sbjct: 649 KAEGGTDNKN-----EAKESDDEEDEDEPEPDTTLFVKNLDFRTTEEQLRKHFSKCGKLH 703

Query: 609 SVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLES 668
             +V+ KKDPK+PG  LSMGYGFV++  +    +ALK LQ S+LD   ++LKRS R L++
Sbjct: 704 YASVSTKKDPKNPGNKLSMGYGFVRYKFKSDCERALKELQTSNLDGKTLDLKRSERTLQT 763

Query: 669 EATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR 728
           +  T  +K+S + +QTG+KILVRN+PFQA   EV+ELFKAFGE+K VRLPKKMVG   HR
Sbjct: 764 DVITTAKKTSKITEQTGTKILVRNVPFQANADEVKELFKAFGEIKSVRLPKKMVGEEKHR 823

Query: 729 GFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
           GFGFVEF TK EAKRA KALCQSTHLYGRRLVLEWA+  + VED+RKRT ++F
Sbjct: 824 GFGFVEFYTKKEAKRAFKALCQSTHLYGRRLVLEWAQTDEGVEDLRKRTAKHF 876

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307192625|gb|EFN75799.1| Probable RNA-binding protein 19 [Harpegnathos saltator]

 Score =  365 bits (936), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 182/347 (52%), Positives = 241/347 (69%), Gaps = 2/347 (0%)

Query: 435 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKN 494
           L+ FNQ  + RS  +ILVKNLP +T P D++ +F   G+LGR+++PP GIT LVEFL+ +
Sbjct: 494 LNTFNQAPKQRSNTVILVKNLPAQTKPADIREMFVKHGELGRIVLPPSGITALVEFLEPS 553

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTA 554
           +A+ AF  LAYTKFK +PLYLEWAP+  F     K KGK   K     EE + E+     
Sbjct: 554 EARKAFTKLAYTKFKHLPLYLEWAPDNSFTAPASKCKGKRDTKKSSNAEEAKGEEATQKE 613

Query: 555 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 614
            ++N     +  +  + D+E EPE DTTL++KN+NF++T + ++ +F KCG +  V +A 
Sbjct: 614 SKENVNNANKKADADDADDE-EPESDTTLFVKNINFSTTTEELKSYFSKCGRLHYVMIAT 672

Query: 615 KKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVK 674
           KKDPK+PG  LSMGYGFV++  +   ++ALK LQ S LD   +ELKRS R L S+  T  
Sbjct: 673 KKDPKNPGNNLSMGYGFVRYKRKYDADRALKTLQMSVLDGKSLELKRSERILTSDVKTA- 731

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
           RK S + +QTG+KILVRN+PFQAK  E+ ELFKAFGELK  RLP+K+VG   HRGF F+E
Sbjct: 732 RKKSKITEQTGTKILVRNVPFQAKAEEITELFKAFGELKATRLPRKLVGFEKHRGFAFIE 791

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
           + TK +AKRA  +LCQSTHLYGRRLVLEWA+  +N+E+IRKRT   F
Sbjct: 792 YHTKEDAKRAFTSLCQSTHLYGRRLVLEWAQAEENLEEIRKRTAERF 838

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	787
FB|FBgn0036018	918	CG3335 [Drosophila melanogaste	0.256	0.220	0.504	2.6e-151
UNIPROTKB|F1NEC5	945	RBM19 "Uncharacterized protein	0.250	0.208	0.55	1.4e-141
ZFIN|ZDB-GENE-031125-3	927	rbm19 "RNA binding motif prote	0.255	0.216	0.544	3e-140
UNIPROTKB|F1RKD1	965	RBM19 "Uncharacterized protein	0.250	0.204	0.53	1.2e-139
MGI|MGI:1921361	952	Rbm19 "RNA binding motif prote	0.250	0.206	0.555	1.5e-138
UNIPROTKB|Q9Y4C8	960	RBM19 "Probable RNA-binding pr	0.250	0.205	0.53	1.9e-138
UNIPROTKB|E2RRF5	968	RBM19 "Uncharacterized protein	0.250	0.203	0.53	3.4e-137
UNIPROTKB|F1P1R2	621	RBM19 "Uncharacterized protein	0.250	0.317	0.55	9.2e-111
UNIPROTKB|F1N0L5	920	RBM19 "Uncharacterized protein	0.250	0.214	0.485	1.3e-110
WB|WBGene00004315	872	rbd-1 [Caenorhabditis elegans	0.260	0.235	0.457	7.5e-110

FB|FBgn0036018 CG3335 [Drosophila melanogaster (taxid:7227)]

 Score = 536 (193.7 bits), Expect = 2.6e-151, Sum P(4) = 2.6e-151
 Identities = 104/206 (50%), Positives = 151/206 (73%)

Query:   580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
             +TTL+++NLNF + ++++ +HF+  G I +V +A+++DP++P +F S+GYGF+QF     
Sbjct:   678 NTTLFLRNLNFKTVQETVEKHFRHLGSIHTVEIAKRRDPENPREFKSLGYGFIQFKKSSV 737

Query:   640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATT-VKRKSSNVAKQTGSKILVRNIPFQAK 698
                ALK LQ + +D + +ELKRS+R L+++     +R+ ++  KQTG+KILVRNIPFQA+
Sbjct:   738 AEHALKNLQLTHIDGNPVELKRSDRVLKTQDNDGAQRRLASQKKQTGTKILVRNIPFQAQ 797

Query:   699 QSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR 757
               EV ++FKAFGEL+ +R+PKK   G   HRGFGFV++++K EAKRA  AL  STHLYGR
Sbjct:   798 YREVRDIFKAFGELRSLRIPKKATTGEDAHRGFGFVDYMSKAEAKRAFDALSASTHLYGR 857

Query:   758 RLVLEWAEEADN--VEDIRKRTNRYF 781
             RLVLEW+   DN  VE++RKRT   F
Sbjct:   858 RLVLEWSANDDNQDVEELRKRTAAKF 883

GO:0004386 "helicase activity" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NEC5 RBM19 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 549 (198.3 bits), Expect = 1.4e-141, Sum P(5) = 1.4e-141
 Identities = 110/200 (55%), Positives = 140/200 (70%)

Query:   582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
             TL+IKNLNF +TE +++  F K G + S T+++KKD    G  LSMG+GFV++   ES  
Sbjct:   718 TLFIKNLNFTTTEGTLKETFSKVGAVKSCTISKKKD--KAGTLLSMGFGFVEYKKPESAQ 775

Query:   642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
             +AL+ LQ   +D H++E+K S R +   A    RK   V KQ  SKILVRNIPFQA   E
Sbjct:   776 KALRRLQGCIVDGHKLEVKISERAVRP-AVKSSRKKQTVKKQKTSKILVRNIPFQATVRE 834

Query:   702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
             + ELF  FGELK VRLPKKM G+G HRGFGFV+F+TK +AK+A  ALC STHLYGRRLVL
Sbjct:   835 IRELFSTFGELKTVRLPKKMAGTGSHRGFGFVDFLTKQDAKKAFNALCHSTHLYGRRLVL 894

Query:   762 EWAEEADNVEDIRKRTNRYF 781
             EWA+  + VE +R+RT  +F
Sbjct:   895 EWADTEETVEALRRRTADHF 914

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IEA

ZFIN|ZDB-GENE-031125-3 rbm19 "RNA binding motif protein 19" [Danio rerio (taxid:7955)]

 Score = 585 (211.0 bits), Expect = 3.0e-140, Sum P(5) = 3.0e-140
 Identities = 111/204 (54%), Positives = 153/204 (75%)

Query:   581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
             +TL+IKNLNF ++E+++++ F KCG + S T+++K+D    G+ LSMGYGFVQ+ T E+ 
Sbjct:   702 STLFIKNLNFITSEETLQKTFSKCGVVKSCTISKKRD--KAGKLLSMGYGFVQYKTPEAA 759

Query:   641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
              +A++ LQ+ ++DEHQ+E+K S R ++S     KRK     KQT SKILVRNIPFQA   
Sbjct:   760 QKAMRQLQHCTVDEHQLEVKISEREVKSGVAQAKRKKQTARKQTTSKILVRNIPFQATVK 819

Query:   701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
             E+ ELF  FGELK VRLPKK +G G HRGFGF++F+TK +AK+A  ALC STHLYGRRLV
Sbjct:   820 ELRELFCTFGELKTVRLPKKGIG-GSHRGFGFIDFLTKQDAKKAFSALCHSTHLYGRRLV 878

Query:   761 LEWAEEADNVEDIRKRTNRYFGTA 784
             LEWA+  + V+D+R++T ++F  A
Sbjct:   879 LEWADAEETVDDLRRKTAQHFHDA 902

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0048546 "digestive tract morphogenesis" evidence=IMP

UNIPROTKB|F1RKD1 RBM19 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 535 (193.4 bits), Expect = 1.2e-139, Sum P(5) = 1.2e-139
 Identities = 106/200 (53%), Positives = 140/200 (70%)

Query:   582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
             TL+IKNLNF++TE++++  F K G + S ++++KK+    G  LSMG+GFV++   E   
Sbjct:   736 TLFIKNLNFSTTEETLKGVFSKVGAVKSCSISKKKN--KAGALLSMGFGFVEYKKPEQAQ 793

Query:   642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
             +ALK LQ   +D H++E++ S R  +  A T  RK     KQT SKILVRNIPFQA   E
Sbjct:   794 KALKQLQGHVVDGHKLEVRISERATKP-APTATRKKQVARKQTTSKILVRNIPFQADSRE 852

Query:   702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
             + ELF  FGELK VRLPKKM G+G HRGFGFV+F TK +AKRA  ALC STHLYGRRLVL
Sbjct:   853 IRELFSTFGELKTVRLPKKMTGTGTHRGFGFVDFFTKQDAKRAFNALCHSTHLYGRRLVL 912

Query:   762 EWAEEADNVEDIRKRTNRYF 781
             EWA+    ++ +R++T  +F
Sbjct:   913 EWADSEVTLQALRRKTAEHF 932

GO:0040019 "positive regulation of embryonic development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1921361 Rbm19 "RNA binding motif protein 19" [Mus musculus (taxid:10090)]

 Score = 554 (200.1 bits), Expect = 1.5e-138, Sum P(5) = 1.5e-138
 Identities = 111/200 (55%), Positives = 144/200 (72%)

Query:   582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
             TL+IKNLNF++TE++++  F K G I S T+++KK+    G  LSMG+GFV++   E   
Sbjct:   723 TLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN--KAGVLLSMGFGFVEYKKPEQAQ 780

Query:   642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
             +ALK LQ  ++D H++E++ S R  +  A T  RK     KQT SKILVRNIPFQA Q E
Sbjct:   781 KALKQLQGHTVDGHKLEVRISERATKP-ALTSTRKKQVPKKQTTSKILVRNIPFQANQRE 839

Query:   702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
             + ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +AK+A  ALC STHLYGRRLVL
Sbjct:   840 IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL 899

Query:   762 EWAEEADNVEDIRKRTNRYF 781
             EWA+    V+ +R++T R+F
Sbjct:   900 EWADSEVTVQTLRRKTARHF 919

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005694 "chromosome" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IMP

UNIPROTKB|Q9Y4C8 RBM19 "Probable RNA-binding protein 19" [Homo sapiens (taxid:9606)]

 Score = 536 (193.7 bits), Expect = 1.9e-138, Sum P(5) = 1.9e-138
 Identities = 106/200 (53%), Positives = 141/200 (70%)

Query:   582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
             TL+IKNLNF++TE+ ++  F K G + S ++++KK+    G  LSMG+GFV++   E   
Sbjct:   731 TLFIKNLNFDTTEEKLKEVFSKVGTVKSCSISKKKN--KAGVLLSMGFGFVEYRKPEQAQ 788

Query:   642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
             +ALK LQ   +D H++E++ S R  +  A T+ RK     KQT SKILVRNIPFQA   E
Sbjct:   789 KALKQLQGHVVDGHKLEVRISERATKP-AVTLARKKQVPRKQTTSKILVRNIPFQAHSRE 847

Query:   702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
             + ELF  FGELK VRLPKKM G+G HRGFGFV+F+TK +AKRA  ALC STHLYGRRLVL
Sbjct:   848 IRELFSTFGELKTVRLPKKMTGTGTHRGFGFVDFLTKQDAKRAFNALCHSTHLYGRRLVL 907

Query:   762 EWAEEADNVEDIRKRTNRYF 781
             EWA+    ++ +R++T  +F
Sbjct:   908 EWADSEVTLQALRRKTAAHF 927

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005654 "nucleoplasm" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS;IDA

GO:0005737 "cytoplasm" evidence=ISS;IDA

GO:0040019 "positive regulation of embryonic development" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|E2RRF5 RBM19 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 543 (196.2 bits), Expect = 3.4e-137, Sum P(5) = 3.4e-137
 Identities = 106/200 (53%), Positives = 146/200 (73%)

Query:   582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
             TL+IKNLNF++TE++++  F K G + S ++++KK+    G+ LSMG+GFV++   E   
Sbjct:   731 TLFIKNLNFSTTEETLKGVFSKAGMVKSCSISKKKN--KAGELLSMGFGFVEYRKPEQAQ 788

Query:   642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
             +ALK LQ   +D H++E++ S R  +  A T  RK     KQT SKILVRNIPFQA + E
Sbjct:   789 KALKQLQGHVVDSHKLEVRISERATKP-ALTSTRKKQVPRKQTTSKILVRNIPFQADKRE 847

Query:   702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
             ++ELF  FGELK VRLPKKM G+G HRGFGFV+F+TK +AKRA +ALC STHLYGRRLVL
Sbjct:   848 IQELFSTFGELKTVRLPKKMTGTGTHRGFGFVDFLTKQDAKRAFQALCHSTHLYGRRLVL 907

Query:   762 EWAEEADNVEDIRKRTNRYF 781
             EWA+   +++ +R++T  +F
Sbjct:   908 EWADSEVSLQALRRKTAEHF 927

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1P1R2 RBM19 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 549 (198.3 bits), Expect = 9.2e-111, Sum P(3) = 9.2e-111
 Identities = 110/200 (55%), Positives = 140/200 (70%)

Query:   582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
             TL+IKNLNF +TE +++  F K G + S T+++KKD    G  LSMG+GFV++   ES  
Sbjct:   394 TLFIKNLNFTTTEGTLKETFSKVGAVKSCTISKKKD--KAGTLLSMGFGFVEYKKPESAQ 451

Query:   642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
             +AL+ LQ   +D H++E+K S R +   A    RK   V KQ  SKILVRNIPFQA   E
Sbjct:   452 KALRRLQGCIVDGHKLEVKISERAVRP-AVKSSRKKQTVKKQKTSKILVRNIPFQATVRE 510

Query:   702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
             + ELF  FGELK VRLPKKM G+G HRGFGFV+F+TK +AK+A  ALC STHLYGRRLVL
Sbjct:   511 IRELFSTFGELKTVRLPKKMAGTGSHRGFGFVDFLTKQDAKKAFNALCHSTHLYGRRLVL 570

Query:   762 EWAEEADNVEDIRKRTNRYF 781
             EWA+  + VE +R+RT  +F
Sbjct:   571 EWADTEETVEALRRRTADHF 590

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IEA

UNIPROTKB|F1N0L5 RBM19 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 495 (179.3 bits), Expect = 1.3e-110, Sum P(4) = 1.3e-110
 Identities = 97/200 (48%), Positives = 139/200 (69%)

Query:   582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
             TL+IKNLNF++TE++++  F K G + S ++++KK+    G  LSMG+GFV++   E   
Sbjct:   691 TLFIKNLNFDTTEETLKGVFSKVGAVKSCSISKKKN--KAGALLSMGFGFVEYRKPEQAQ 748

Query:   642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
             +ALK LQ   +D H++E++ S R  +S   + + K S   +QT +KI VR  PFQ    E
Sbjct:   749 KALKQLQGHVVDGHKLEVRISERATKSALNSGRHKHSP-RRQTDTKIWVRVCPFQGDSRE 807

Query:   702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
             ++E+F  FGELK VRLPKK+ G+G HRGFGFV+F+TK +AKRA  ALC STHLYGRRLVL
Sbjct:   808 LKEIFNTFGELKTVRLPKKLTGTGTHRGFGFVDFLTKQDAKRAFNALCHSTHLYGRRLVL 867

Query:   762 EWAEEADNVEDIRKRTNRYF 781
             EWA+   ++  +R++T  +F
Sbjct:   868 EWADSEVSLPALRRKTAEHF 887

GO:0040019 "positive regulation of embryonic development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

WB|WBGene00004315 rbd-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 453 (164.5 bits), Expect = 7.5e-110, Sum P(4) = 7.5e-110
 Identities = 97/212 (45%), Positives = 141/212 (66%)

Query:   581 TTLYIKNLNFNSTEDSIRRHFKK-CGPIA-SVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
             +TL++KNL F++T+ S+   F+K  G +  S  +++K +P  P + LSMG+GFVQFYT  
Sbjct:   641 STLFVKNLAFDTTDGSLEFLFRKRYGDLVKSAQISKKLNPAEPTKPLSMGFGFVQFYTAF 700

Query:   639 SLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG--SKILVRNIPFQ 696
                 ALK +Q   LD H +ELK S+R   ++   +KRK     K+ G  +K+LVRN+PF+
Sbjct:   701 DAKTALKDMQGELLDGHSLELKISHRE-NADKGALKRKEVK-QKEQGECTKLLVRNLPFE 758

Query:   697 AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
             A   EVE LF+ FG +K +R+PKK      HRGFGFV+FI+ +EA RA  +L  STHLYG
Sbjct:   759 ASVKEVETLFETFGAVKTIRIPKKPGQKQQHRGFGFVDFISADEAHRAFDSLVHSTHLYG 818

Query:   757 RRLVLEWAEEADNVEDIRKRT-NRYFGTAVGL 787
             RRLVLEWA++ + VE++R++T  ++ G   G+
Sbjct:   819 RRLVLEWAKDDETVEELREKTAEKFAGNKKGV 850

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0006396 "RNA processing" evidence=IMP

GO:0040039 "inductive cell migration" evidence=IMP

GO:0005730 "nucleolus" evidence=IDA

GO:0000478 "endonucleolytic cleavage involved in rRNA processing" evidence=IMP

GO:0040025 "vulval development" evidence=IMP

GO:0040002 "collagen and cuticulin-based cuticle development" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8R3C6	RBM19_MOUSE	No assigned EC number	0.5113	0.4371	0.3613	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	787
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-44
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	7e-40
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-35
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-35
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	5e-33
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-31
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	5e-31
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	1e-29
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	9e-25
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	3e-24
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-22
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-21
smart00360	73	smart00360, RRM, RNA recognition motif	2e-21
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	6e-20
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-19
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	5e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-17
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-16
smart00360	73	smart00360, RRM, RNA recognition motif	2e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-16
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-16
smart00360	73	smart00360, RRM, RNA recognition motif	1e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-15
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-15
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-15
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-15
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-14
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-14
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-13
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-13
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-13
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	8e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-12
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-12
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	8e-12
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	9e-12
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-12
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-11
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-11
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-11
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	6e-11
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	7e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-10
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-10
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-10
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-10
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-10
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	9e-10
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	9e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-09
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-09
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-09
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	4e-09
smart00360	73	smart00360, RRM, RNA recognition motif	5e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-09
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	5e-09
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	6e-09
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-09
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	7e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-09
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	8e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	8e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-09
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	9e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-08
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	2e-08
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-08
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-08
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-08
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-08
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-08
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	3e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-08
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-08
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-08
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-08
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-08
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	6e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	7e-08
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	7e-08
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-08
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	9e-08
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-07
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-07
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-07
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	3e-07
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	5e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-07
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-07
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	5e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	6e-07
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-07
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	7e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	8e-07
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	8e-07
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	8e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-07
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	9e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-06
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	2e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-06
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-06
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-06
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-06
smart00360	73	smart00360, RRM, RNA recognition motif	3e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-06
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-06
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	4e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	5e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-06
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	5e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	6e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-06
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	7e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	7e-06
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	7e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	8e-06
smart00360	73	smart00360, RRM, RNA recognition motif	9e-06
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	9e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	1e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	1e-05
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	2e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	2e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	2e-05
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	2e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	2e-05
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	2e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-05
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	2e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-05
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	3e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	3e-05
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	3e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-05
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	4e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	4e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	5e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-05
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	5e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	5e-05
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	5e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	6e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	7e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	7e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	7e-05
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	7e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	7e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	8e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	8e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	8e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	8e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	9e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	9e-05
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	9e-05
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	9e-05
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	1e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	1e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-04
cd12513	81	cd12513, RRM3_RBM12B, RNA recognition motif 3 in R	1e-04
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	1e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	1e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	2e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-04
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	2e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	2e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-04
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	2e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	3e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	3e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	3e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	3e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	3e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	3e-04
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-04
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	4e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	4e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-04
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	4e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	4e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	4e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	4e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	5e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	5e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	5e-04
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	5e-04
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	5e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	5e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	5e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	5e-04
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	5e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	5e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	6e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	6e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	6e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	6e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	6e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	6e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	7e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	7e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	7e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	7e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	7e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	7e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	8e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	8e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	8e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	8e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	8e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	8e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	8e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	9e-04
cd12434	75	cd12434, RRM_RCAN_like, RNA recognition motif in r	9e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.001
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.001
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.001
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.001
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.001
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.001
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	0.001
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.001
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.001
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.001
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	0.001
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.001
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.001
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.001
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.001
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.001
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.001
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.001
cd12308	79	cd12308, RRM1_Spen, RNA recognition motif 1 in the	0.001
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.001
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.001
cd12753	85	cd12753, RRM1_RBM10, RNA recognition motif 1 in ve	0.001
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.001
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.001
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.001
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.001
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.001
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.001
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.001
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.002
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.002
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.002
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	0.002
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.002
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.002
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.002
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.002
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.002
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.002
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.002
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.002
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.002
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.002
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.002
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	0.002
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.002
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.002
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.002
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.002
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.003
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.003
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.003
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	0.003
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.003
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.003
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	0.003
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.003
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.003
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.003
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.003
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.003
cd12693	96	cd12693, RRM2_PTBP1_like, RNA recognition motif 2	0.003
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	0.003
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	0.003
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	0.003
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.004
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.004
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	0.004
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.004
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.004
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.004
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	0.004
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.004
cd12502	72	cd12502, RRM2_RMB19, RNA recognition motif 2 in RN	0.004
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	0.004
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	0.004
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.004
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	0.004
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	0.004
cd12752	87	cd12752, RRM1_RBM5, RNA recognition motif 1 in ver	0.004

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score =  154 bits (392), Expect = 1e-44
 Identities = 62/79 (78%), Positives = 67/79 (84%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           SKILVRNIPF+A   E+ ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +AKRA 
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 746 KALCQSTHLYGRRLVLEWA 764
           KALC STHLYGRRLVLEWA
Sbjct: 61  KALCHSTHLYGRRLVLEWA 79

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score =  141 bits (356), Expect = 7e-40
 Identities = 54/79 (68%), Positives = 66/79 (83%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ESGR+F+RNL+YT TE+DL KLF KYGPL+EV LPIDK T K KGFA VT+++PEHA +A
Sbjct: 1   ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 395 YQHLDGTVFLGRMLHLIPG 413
           +  LDGTVF GR+LHL+P 
Sbjct: 61  FAELDGTVFQGRLLHLLPS 79

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score =  128 bits (323), Expect = 3e-35
 Identities = 48/82 (58%), Positives = 68/82 (82%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           TTL++KNLNF +TE+++++HF+KCG + SVT+A+KKDPK PG+ LSMGYGFV+F ++E+ 
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 641 NQALKVLQNSSLDEHQIELKRS 662
            +ALK LQ + LD H +ELK S
Sbjct: 61  QKALKRLQGTVLDGHALELKLS 82

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score =  126 bits (320), Expect = 7e-35
 Identities = 50/79 (63%), Positives = 64/79 (81%), Gaps = 3/79 (3%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           +K++VRN+PF+A + E+ ELF  FG++K VRLPKK  GS  HRGF FVEF+TK EA+ AM
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGS--HRGFAFVEFVTKQEAQNAM 58

Query: 746 KALCQSTHLYGRRLVLEWA 764
           +AL +STHLYGR LVLE+A
Sbjct: 59  EAL-KSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score =  121 bits (305), Expect = 5e-33
 Identities = 47/71 (66%), Positives = 56/71 (78%)

Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
           +ILVKNLP  TL  +L+ LF  FG LGRVL+PP GIT +VEFL+ ++AK AF  LAY+KF
Sbjct: 2   VILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGITAIVEFLEPSEAKLAFRKLAYSKF 61

Query: 509 KEVPLYLEWAP 519
           K VPLYLEWAP
Sbjct: 62  KHVPLYLEWAP 72

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score =  115 bits (291), Expect = 4e-31
 Identities = 42/73 (57%), Positives = 60/73 (82%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FVRNL +T TE++L +LFE +G ++EV LP+DKET ++KGFA V+F+ PEHA +AY  
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 398 LDGTVFLGRMLHL 410
           LDG++F GR+LH+
Sbjct: 61  LDGSIFQGRLLHV 73

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score =  115 bits (291), Expect = 5e-31
 Identities = 47/79 (59%), Positives = 62/79 (78%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           E+GR+FVRNL Y+  EDDL KLF K+G L+EV + IDK++ K+KGFA V FL PE A +A
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 395 YQHLDGTVFLGRMLHLIPG 413
           Y+ LDG VF GR++H++PG
Sbjct: 61  YKELDGKVFQGRLIHILPG 79

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score =  111 bits (281), Expect = 1e-29
 Identities = 43/72 (59%), Positives = 53/72 (73%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
            +ILVKNLP+ T   +L+ LFE FG LGR+L+PP     LVEFL+ + A+ AF SLAY +
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKR 60

Query: 508 FKEVPLYLEWAP 519
           FK VPLYLEWAP
Sbjct: 61  FKHVPLYLEWAP 72

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 98.1 bits (245), Expect = 9e-25
 Identities = 35/66 (53%), Positives = 51/66 (77%)

Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           I +++L+  FE  GT+TDVQLKYT +GKFR+F F+GY  E++AQ AL +FNN+++ +S+
Sbjct: 11 GIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSK 70

Query: 88 IKVEKC 93
          I VE C
Sbjct: 71 ITVEIC 76

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 96.3 bits (240), Expect = 3e-24
 Identities = 38/70 (54%), Positives = 46/70 (65%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
           ILVKN PY T   +L+ LFEP G L RVL+PP G   +VEF    QA+ AF +LAY +FK
Sbjct: 3   ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRRFK 62

Query: 510 EVPLYLEWAP 519
           +  LYLE  P
Sbjct: 63  DSILYLEKGP 72

This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 91.0 bits (226), Expect = 2e-22
 Identities = 44/79 (55%), Positives = 57/79 (72%), Gaps = 3/79 (3%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           +KILV+N+PF+A + +V  LF ++G+LK VR+PKK   S   RGF FVEF T  EA  AM
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA--RGFAFVEFSTAKEALNAM 58

Query: 746 KALCQSTHLYGRRLVLEWA 764
            AL + THL GRRLVL++A
Sbjct: 59  NAL-KDTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 99.1 bits (247), Expect = 2e-21
 Identities = 105/454 (23%), Positives = 165/454 (36%), Gaps = 115/454 (25%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V +L   VTE  L  LF+ +GP+  V +  D  T ++ G+  V F  P  A +A + +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 399 DGTVFLGRMLHLI-----PGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK 453
           +     G+ + ++     P   +   GN                            I VK
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVGN----------------------------IFVK 94

Query: 454 NLPYRTLPTDLKALFEPFGDLGRVL-----VPPYGIT---GLVEFLQKNQAKAAFNSLAY 505
           NL       D KALF+ F   G +L         G +   G V F ++  AKAA   +  
Sbjct: 95  NLDKSV---DNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKV-- 149

Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
                          G+    KE   G+  +K+E E    ++                  
Sbjct: 150 --------------NGMLLNDKEVYVGRFIKKHEREAAPLKKF----------------- 178

Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
                          T LY+KNL+ +  ED +R  F K G I S  V   KD        
Sbjct: 179 ---------------TNLYVKNLDPSVNEDKLRELFAKFGEITSAAV--MKDGSG----R 217

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE-----------HQIELKRSNRNLESEATTVK 674
           S G+ FV F   E   +A++ +    +              Q   KR+ R  E      +
Sbjct: 218 SRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQ---KRAEREAELRRKFEE 274

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
            +     K  G  + V+N+       ++ ELF   GE+   ++   +   G+ RGFGFV 
Sbjct: 275 LQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKV--MLDEKGVSRGFGFVC 332

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD 768
           F    EA RA+  +     L G+ L +  A+  +
Sbjct: 333 FSNPEEANRAVTEM-HGRMLGGKPLYVALAQRKE 365

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 88.4 bits (220), Expect = 2e-21
 Identities = 32/73 (43%), Positives = 43/73 (58%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +FV NL    TE++L +LF K+G +  V L  DKET K+KGFA V F   E A +A + 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 398 LDGTVFLGRMLHL 410
           L+G    GR L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 84.2 bits (209), Expect = 6e-20
 Identities = 30/63 (47%), Positives = 46/63 (73%)

Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
          +T+++L+  FE KG VTDV++  T +GK RRF F+G+  E+ AQ A+ YFN T++ +S+I
Sbjct: 12 VTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKI 71

Query: 89 KVE 91
           VE
Sbjct: 72 SVE 74

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 83.0 bits (205), Expect = 2e-19
 Identities = 37/83 (44%), Positives = 48/83 (57%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL++KNLNF++T   +   FK         V  K DPK PGQ LSMG+GFV F T+E   
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 642 QALKVLQNSSLDEHQIELKRSNR 664
            ALK +    LD H + +K S+R
Sbjct: 62  AALKAMDGFVLDGHTLVVKFSHR 84

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 78.8 bits (195), Expect = 5e-18
 Identities = 34/67 (50%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 28 KITQEQLKAKFEEK-GTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           +T+ +LK  F +  G +TDV+L  T +GK RR AFIGY  E++AQ A DYFNNTY+ +S
Sbjct: 11 SLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNNTYINTS 70

Query: 87 RIKVEKC 93
          +I VE  
Sbjct: 71 KISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 75.4 bits (186), Expect = 7e-17
 Identities = 31/72 (43%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL    TE+DL +LF K+G +  V +  DK   K+KGFA V F  PE A +A + L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 399 DGTVFLGRMLHL 410
           +G    GR L +
Sbjct: 60  NGKELDGRKLKV 71

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 83.3 bits (206), Expect = 1e-16
 Identities = 99/432 (22%), Positives = 153/432 (35%), Gaps = 101/432 (23%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-------LGMAYIGFKDEKNCNKALNK 277
           ++ V +L   V +  L   FKP  P+ SVR          LG  Y+ F++  +  +AL  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 278 -NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAES 336
            N     GK + I    +D S + SG                                  
Sbjct: 62  MNFKRLGGKPIRIMWSQRDPSLRRSG---------------------------------V 88

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           G IFV+NL  +V    L   F K+G +    +  D E  K++G+  V F   E A  A Q
Sbjct: 89  GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQ 147

Query: 397 HLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLP 456
            ++G +   + +++     K                  L  F  +          VKNL 
Sbjct: 148 KVNGMLLNDKEVYVGRFIKKHEREA-----------APLKKFTNL---------YVKNLD 187

Query: 457 YRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE 516
                  L+ LF  FG           IT        +     F  + + K ++    +E
Sbjct: 188 PSVNEDKLRELFAKFG----------EITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVE 237

Query: 517 WAPEGVFAEAKEKSK---GKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE 573
                    AKE  K   G+ +++ E E E   + ++     +   QGV           
Sbjct: 238 EMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGV----------- 286

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
                    LY+KNL+   T++ +R  F +CG I S  V    D K     +S G+GFV 
Sbjct: 287 --------NLYVKNLDDTVTDEKLRELFSECGEITSAKVML--DEKG----VSRGFGFVC 332

Query: 634 FYTRESLNQALK 645
           F   E  N+A+ 
Sbjct: 333 FSNPEEANRAVT 344

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 74.2 bits (183), Expect = 2e-16
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 5/78 (6%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL++ NL  ++TE+ +R  F K G + SV + R K+        S G+ FV+F + E   
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGK-----SKGFAFVEFESEEDAE 55

Query: 642 QALKVLQNSSLDEHQIEL 659
           +AL+ L    LD   +++
Sbjct: 56  KALEALNGKELDGRPLKV 73

Length = 73

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 80.4 bits (197), Expect = 2e-16
 Identities = 66/267 (24%), Positives = 112/267 (41%), Gaps = 5/267 (1%)

Query: 265 FKDEKNCNKALNKNKSFWKG---KQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWK 321
              E N      K +S       K+L   +  ++N  +     D     + E  +     
Sbjct: 42  NSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRS 101

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
           S+    +  +   E+  +FV NL Y VTE+DL +LF+K+GP+  V L  D+ET K++GFA
Sbjct: 102 SESPKSR-QKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFA 160

Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQV 441
            V F   E A +A + L+G    GR L +   +P       +   +   S  K  +  + 
Sbjct: 161 FVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ-PRSELSNNLDASFAKKLSRGKA 219

Query: 442 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
           +       + V NLP +T   +L  LF+  GD+ R  +PP     + +       +A+ +
Sbjct: 220 LLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKD 279

Query: 502 SLAYTKFKEVPLYLEWAPEGVFAEAKE 528
           +L           L   P   F++ + 
Sbjct: 280 ALESNSRGNKKKILGRGPRKAFSQPRL 306

Length = 306

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 73.8 bits (182), Expect = 3e-16
 Identities = 29/72 (40%), Positives = 42/72 (58%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
            ++FV  LS   TE +L  LF K+G + EV+L  D ET +++GF  VTF   E A  A +
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 397 HLDGTVFLGRML 408
            L+G    GR++
Sbjct: 62  DLNGKELEGRVI 73

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 2/75 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V N+P    + E+ ELF  FG+++ VRL +    +G  +GF FVEF ++ +A++A++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKE-TGKSKGFAFVEFESEEDAEKALE 59

Query: 747 ALCQSTHLYGRRLVL 761
           AL     L GR L +
Sbjct: 60  AL-NGKELDGRPLKV 73

Length = 73

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 30/71 (42%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL    TE+DL  LF K+GP+  + +  D ET ++KGFA V F   E A +A + L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 399 DGTVFLGRMLH 409
           +G    GR L 
Sbjct: 60  NGKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 70.7 bits (174), Expect = 3e-15
 Identities = 29/78 (37%), Positives = 43/78 (55%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRNL Y  T++ L + F + GP+    +  DK + K +GF  VTF + E A +A +  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 399 DGTVFLGRMLHLIPGKPK 416
             T F GR +H+   K K
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 77.7 bits (191), Expect = 3e-15
 Identities = 54/175 (30%), Positives = 81/175 (46%), Gaps = 20/175 (11%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           E  T L +  L    T++ IR  F   G I S  + R K     GQ  S+GYGFV +   
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK---VTGQ--SLGYGFVNYVRP 55

Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA 697
           E   +A+  L    L    I++            +  R SS+  K  G+ + V  +P   
Sbjct: 56  EDAEKAVNSLNGLRLQNKTIKV------------SYARPSSDSIK--GANLYVSGLPKTM 101

Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST 752
            Q E+E +F  FG++   R+    V +GL +G GF+ F  ++EA RA+K L  +T
Sbjct: 102 TQHELESIFSPFGQIITSRILSDNV-TGLSKGVGFIRFDKRDEADRAIKTLNGTT 155

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 70.3 bits (173), Expect = 4e-15
 Identities = 31/70 (44%), Positives = 42/70 (60%), Gaps = 2/70 (2%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++VRNL  +VTE+DL + F  YG +  V L  +K  D+ +GFA V F  PE A  A + L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 399 DGTVFLGRML 408
           +G V  GR L
Sbjct: 59  NGLVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 69.3 bits (170), Expect = 1e-14
 Identities = 30/70 (42%), Positives = 43/70 (61%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++VRN++     DDL +LF KYGP+ +V +P+D  T + +GFA V F     A  A  +L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 399 DGTVFLGRML 408
           D T FLGR +
Sbjct: 63  DRTRFLGREI 72

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++ NL  ++TE+ +R  F K G I SV + R KD K      S G+ FV+F + E   +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK------SKGFAFVEFESPEDAEK 54

Query: 643 ALKVLQNSSLDEHQIELK 660
           AL+ L    LD  ++++ 
Sbjct: 55  ALEALNGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 28/71 (39%), Positives = 41/71 (57%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            ++V NL Y VTE+DL  LF ++G +    +  D+ET +++GF  V     E A  A + 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 398 LDGTVFLGRML 408
           L+GT F GR L
Sbjct: 61  LNGTDFGGRTL 71

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 68.7 bits (168), Expect = 2e-14
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           G++F+  LS+   E  L ++F KYG ++EV++  D+ET +++GF  VTF  P+ A  A  
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 397 HLDGTVFLGRML 408
            ++G    GR +
Sbjct: 61  AMNGKSVDGRQI 72

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 26/78 (33%), Positives = 51/78 (65%), Gaps = 3/78 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           +++VRN+PF+  ++++++LF  FG +  V +P+K    G  +GF FV+F +K +A++A+K
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP--DGKKKGFAFVQFTSKADAEKAIK 58

Query: 747 ALCQSTHLYGRRLVLEWA 764
                  + GR + ++WA
Sbjct: 59  G-VNGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 67.9 bits (167), Expect = 3e-14
 Identities = 30/63 (47%), Positives = 40/63 (63%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            I V NLS    EDDL +LF  +GP++ V L  DKET +++GFA VTF   E A +A + 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 398 LDG 400
           L+G
Sbjct: 61  LNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 73.4 bits (179), Expect = 4e-14
 Identities = 54/235 (22%), Positives = 98/235 (41%), Gaps = 21/235 (8%)

Query: 527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE-----REPEPDT 581
            E S   +K     E +E  E + E   + +        EE     E      +  E + 
Sbjct: 57  SEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENN 116

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL++ NL ++ TE+ +R  FKK GP+  V + R ++        S G+ FV+F + ES  
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGK-----SRGFAFVEFESEESAE 171

Query: 642 QALKVLQNSSLDEHQIELK--------RSNRNLESEATTVKRKSSNVAKQT--GSKILVR 691
           +A++ L    L+   + ++        RS  +   +A+  K+ S   A        + V 
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           N+P +  + E+ +LFK+ G++    LP       + +   FV      +A  +  
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSK-DGKIPKSRSFVGNEASKDALESNS 285

Length = 306

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 65.0 bits (159), Expect = 3e-13
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 3/75 (4%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V N+P    + ++ ELF  FGE++ VR+ +   G    +GF FVEF +  +A++A++A
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK--SKGFAFVEFESPEDAEKALEA 58

Query: 748 LCQSTHLYGRRLVLE 762
           L     L GR+L + 
Sbjct: 59  L-NGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 65.0 bits (159), Expect = 4e-13
 Identities = 28/70 (40%), Positives = 43/70 (61%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL +++T +DL K+F KYG + +V +  DKET K+KG A + FL  E A +  + L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 399 DGTVFLGRML 408
           +     GR L
Sbjct: 64  NNKELFGRTL 73

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 64.2 bits (157), Expect = 6e-13
 Identities = 29/68 (42%), Positives = 40/68 (58%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V NL+Y  T DDL ++FEKYG + +V +P D+ T +++GFA V F     A  A   +DG
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 401 TVFLGRML 408
               GR L
Sbjct: 63  KELDGREL 70

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 71.1 bits (174), Expect = 8e-13
 Identities = 49/215 (22%), Positives = 90/215 (41%), Gaps = 34/215 (15%)

Query: 200 KSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYF-KPLPLASVRTTF- 257
           +  D      +  P+++A   +R   T+ V  L    +++DL  +F K   +  V+    
Sbjct: 68  RRDDRRSGRNTKEPLTEA---ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKD 124

Query: 258 ------LGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNAS 311
                  G+AY+ F D ++  KAL        G+ + +           S  A+ N  A 
Sbjct: 125 RNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ----------SSQAEKNRAAK 174

Query: 312 MENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPID 371
               +     +               +++V NL + +TE +L ++FE +G + +V L  D
Sbjct: 175 AATHQPGDIPNFL-------------KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRD 221

Query: 372 KETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR 406
            ET ++KGF  + F   E A +A + ++G    GR
Sbjct: 222 PETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGR 256

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 62.4 bits (152), Expect = 2e-12
 Identities = 29/72 (40%), Positives = 40/72 (55%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NLS+   ED + + F +YG ++ V LP D ++ + KGF  V F   E A  A   L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 399 DGTVFLGRMLHL 410
            GT  LGR + L
Sbjct: 61  GGTDLLGRPVRL 72

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 62.6 bits (153), Expect = 3e-12
 Identities = 23/71 (32%), Positives = 36/71 (50%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +F+RNL +  TE++L +LF ++G +    +  DK T  +KG A V F   E A +  +  
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 399 DGTVFLGRMLH 409
           D     G  L 
Sbjct: 63  DNAEDSGLSLD 73

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 26/70 (37%), Positives = 39/70 (55%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV N+ Y  TE+ L ++F + GP+    L  D++T K KG+    F   E A  A ++L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 399 DGTVFLGRML 408
           +G  F GR L
Sbjct: 61  NGYEFNGRAL 70

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 61.9 bits (151), Expect = 4e-12
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IFV  L Y  T+D L K F ++G + E ++  D++T K++G+  VTF   E A +A + 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 398 LDGTVFLGRMLHL 410
            +  +  GR  ++
Sbjct: 62  PN-PIIDGRKANV 73

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 26/70 (37%), Positives = 41/70 (58%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL + +TEDDL  +FE +G +  V L  D ET ++KG+  + F   E A +A + L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 399 DGTVFLGRML 408
           +G    GR +
Sbjct: 61  NGFELAGRPI 70

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 61.5 bits (150), Expect = 6e-12
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++ NL  ++TE+ ++  F K GPI S+ + R +  +      S G+ FV+F   E   +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR------SKGFAFVEFEDEEDAEK 54

Query: 643 ALKVLQNSSLDEHQIE 658
           AL+ L    L   ++ 
Sbjct: 55  ALEALNGKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 61.0 bits (149), Expect = 8e-12
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ NL+F +TE+ I   F +CG I  + +   +  K+P      G+ FV++YTRE    
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTP-----CGFCFVEYYTREDAEN 55

Query: 643 ALKVLQNSSLDEHQI 657
           A+K L  + LD+  I
Sbjct: 56  AVKYLNGTKLDDRII 70

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 61.1 bits (149), Expect = 9e-12
 Identities = 29/69 (42%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ VRNL +  TE DL KLF  +G + EV +P  K   K KGFA V F     A +A + 
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIP-RKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 398 LDGTVFLGR 406
           ++G    GR
Sbjct: 60  VNGKKIKGR 68

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 60.9 bits (148), Expect = 9e-12
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +FV NLS++V ++ L   FEK+G +    +  D+ET +++GF  V F  PE A +A + 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 398 LDGTVFLGRMLHL 410
           +DG    GR +++
Sbjct: 61  MDGKELDGRPINV 73

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTK---GFALVTFLMPEHATQAY 395
           I+VRNL + + EDDL  +F K+G +  + +P  ++  + +   GFA VTF     A  A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 396 QHLDGTVFLGRMLH 409
           Q L+GT   GR + 
Sbjct: 63  Q-LNGTELGGRKIS 75

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 4/75 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK--MVGSGLHRGFGFVEFITKNEAKRA 744
           +I VRN+ F+  + ++  +F  FGE++ +R+PKK       L+ GF FV F   + A+ A
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 745 MKALCQSTHLYGRRL 759
           ++     T L GR++
Sbjct: 62  LQL--NGTELGGRKI 74

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 59.1 bits (144), Expect = 3e-11
 Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 7/76 (9%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY++NL  + TE+ +R  F   G +  V + R KD          G+ FV+F + E    
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPR-------GFAFVEFASPEDAEA 53

Query: 643 ALKVLQNSSLDEHQIE 658
           ALK L    LD   + 
Sbjct: 54  ALKKLNGLVLDGRTLR 69

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 58.9 bits (143), Expect = 4e-11
 Identities = 17/65 (26%), Positives = 33/65 (50%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             T+E L+  F + G +  V++    +GK + FAF+ +   + A+ AL+  N   +   
Sbjct: 8  PDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGR 67

Query: 87 RIKVE 91
          ++KV 
Sbjct: 68 KLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 59.1 bits (143), Expect = 5e-11
 Identities = 28/78 (35%), Positives = 45/78 (57%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRNL+++VT++DLT  F    P+   ++  D ET +++G+  VTF M E A +A   L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 399 DGTVFLGRMLHLIPGKPK 416
                 GR+L L   + +
Sbjct: 62  KNKKLHGRILRLDIAERR 79

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 58.8 bits (143), Expect = 5e-11
 Identities = 23/71 (32%), Positives = 38/71 (53%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L+  V E  L   F  +G + ++ +P+D ET K +GFA V F  PE A  A  ++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 399 DGTVFLGRMLH 409
           + +   GR + 
Sbjct: 61  NESELFGRTIR 71

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 6/60 (10%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I V+NL +  TE++L +LFEK+G L  ++LP       ++  ALV FL P  A +A++ L
Sbjct: 3   ILVKNLPFGTTEEELRELFEKFGSLGRLLLP------PSRTIALVEFLEPSDARKAFKSL 56

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 58.5 bits (142), Expect = 7e-11
 Identities = 30/72 (41%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL   VTE+ L +LF + GPL  V +P D    K K FA VTF        A Q L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQLL 62

Query: 399 DGTVFLGRMLHL 410
           +G    GR L +
Sbjct: 63  NGIRLFGRELRI 74

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 64.4 bits (157), Expect = 1e-10
 Identities = 67/310 (21%), Positives = 120/310 (38%), Gaps = 57/310 (18%)

Query: 227 IVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL------GMAYIGFKDEKNCNKALNKNK 279
           I VKNL   V  K L   F     + S +          G  ++ F+ E++   A+ K  
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK-- 148

Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRI 339
                  +N             G   ++    +     KH +      +F         +
Sbjct: 149 -------VN-------------GMLLNDKEVYVGRFIKKHEREAAPLKKFTN-------L 181

Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
           +V+NL  +V ED L +LF K+G +    +  D  + +++GFA V F   E A +A + ++
Sbjct: 182 YVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 400 GTVF----LGRMLHLIPGKPK-ENEGNVDGKVHCCISERKLDAFNQVVEARSKRI-ILVK 453
           G        G+ L++   + + E E             RK +   Q  + +++ + + VK
Sbjct: 241 GKKIGLAKEGKKLYVGRAQKRAEREA---------ELRRKFEELQQERKMKAQGVNLYVK 291

Query: 454 NLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYTKF 508
           NL        L+ LF   G++   +V++   G++   G V F    +A  A   +     
Sbjct: 292 NLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRML 351

Query: 509 KEVPLYLEWA 518
              PLY+  A
Sbjct: 352 GGKPLYVALA 361

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 63.8 bits (155), Expect = 1e-10
 Identities = 48/235 (20%), Positives = 105/235 (44%), Gaps = 22/235 (9%)

Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEER----EPEPDT 581
           ++ +S+ +++ +   + +     +  + +   N+   P  + +   D+ R      EP T
Sbjct: 24  SRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLT 83

Query: 582 -------TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                  T+++  L   + E  +   F K G +  V   + ++ +      S G  +V+F
Sbjct: 84  EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRR-----SKGVAYVEF 138

Query: 635 YTRESLNQALKVLQNSSLDEH-QIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNI 693
           Y  ES+ +AL +     L     ++  ++ +N  ++A T              K+ V N+
Sbjct: 139 YDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAAT----HQPGDIPNFLKLYVGNL 194

Query: 694 PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
            F   + E+ ++F+ FG+++ V+L +     G  +GFGF++F    EAK A++ +
Sbjct: 195 HFNITEQELRQIFEPFGDIEDVQLHRDPET-GRSKGFGFIQFHDAEEAKEALEVM 248

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 25/62 (40%), Positives = 39/62 (62%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + V  L+  V +D L ++F  YG + +V LPID+E +  +G+A V F  PE A +A +H+
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 399 DG 400
           DG
Sbjct: 61  DG 62

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 3/72 (4%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V N+P    + ++++LF  FG ++ +R+ +    +G  +GF FVEF  + +A++A++A
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD--ETGRSKGFAFVEFEDEEDAEKALEA 58

Query: 748 LCQSTHLYGRRL 759
           L     L GR L
Sbjct: 59  L-NGKELGGREL 69

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 57.6 bits (140), Expect = 2e-10
 Identities = 29/81 (35%), Positives = 47/81 (58%), Gaps = 6/81 (7%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + VRN+P+     ++EE F   G +K  FV   K   GS   RGFG+V F  + +AKRA+
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDK---GSKKCRGFGYVTFALEEDAKRAL 58

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
           +   + T   GR++ +E+A++
Sbjct: 59  EEK-KKTKFGGRKIHVEFAKK 78

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + VRN+P    + ++ E F  +G+++ VRL +        RGF FVEF +  +A+ A+K 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN---KDRPRGFAFVEFASPEDAEAALKK 57

Query: 748 LCQSTHLYGRRL 759
                 L GR L
Sbjct: 58  -LNGLVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAM 745
            + V N+P+   + ++++LF  FGE+   R+   +   +G  RGFGFVE  T  EA  A+
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRE--TGRSRGFGFVEMETAEEANAAI 58

Query: 746 KALCQSTHLYGRRLVLEWAE 765
           + L   T   GR L +  A 
Sbjct: 59  EKL-NGTDFGGRTLTVNEAR 77

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 56.8 bits (138), Expect = 3e-10
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 5/78 (6%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV----GSGLHRGFGFVEFITKNEAKR 743
           + V+N+ F+  +  +++ F+  G ++ V + KK      G  L  G+GFVEF +K  A++
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 744 AMKALCQSTHLYGRRLVL 761
           A+K L Q T L G  L L
Sbjct: 63  ALKRL-QGTVLDGHALEL 79

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 56.4 bits (137), Expect = 4e-10
 Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 6/79 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           ++++ NL F+  E+ +R+HF+ CG + +V + R  D K+    +  G+G+V F T++S+ 
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVR--DRKTG---IGKGFGYVLFKTKDSVA 55

Query: 642 QALKVLQNSSLDEHQIELK 660
            ALK L    L   +I +K
Sbjct: 56  LALK-LNGIKLKGRKIRVK 73

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 55.8 bits (135), Expect = 5e-10
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 4/79 (5%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V N+ + A+Q ++EE FK  GE+  VR+ +   G    +GFG VEF T+  A++A++ 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRS--KGFGHVEFATEEGAQKALEK 59

Query: 748 LCQSTHLYGRRLVLEWAEE 766
                 L GR + ++ A E
Sbjct: 60  --SGEELLGREIRVDLATE 76

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 55.8 bits (135), Expect = 6e-10
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL++ NL++++ +D +   FK+CG +  V +A+  D +S       G+G V+F T E   
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSK------GFGHVEFATEEGAQ 54

Query: 642 QALKVLQNSSLDEHQI 657
           +AL+      L   +I
Sbjct: 55  KALE-KSGEELLGREI 69

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 56.1 bits (136), Expect = 6e-10
 Identities = 26/68 (38%), Positives = 38/68 (55%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  L+Y  TE  L + FE+YGP+  + L  DK+T K +G+A + F        AY++ 
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 399 DGTVFLGR 406
           DG    GR
Sbjct: 64  DGKKIDGR 71

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 55.6 bits (134), Expect = 9e-10
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + VRN+ F   Q ++ + F     +K   V    +   +G  RG+GFV F    +A+ A+
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPE---TGESRGYGFVTFAMLEDAQEAL 58

Query: 746 KALCQSTHLYGRRLVLEWAE 765
             L ++  L+GR L L+ AE
Sbjct: 59  AKL-KNKKLHGRILRLDIAE 77

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 56.5 bits (136), Expect = 9e-10
 Identities = 27/92 (29%), Positives = 38/92 (41%), Gaps = 4/92 (4%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL----MPEHATQA 394
           +FVRNL Y  TE+ L   F K+G +   +  IDK T + KG   V F            A
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGKV 426
                 ++  G  L    G     E  ++G+V
Sbjct: 64  PAAGSTSLLSGSSLTADIGDDVMPEYVLEGRV 95

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 61.4 bits (149), Expect = 1e-09
 Identities = 86/415 (20%), Positives = 160/415 (38%), Gaps = 72/415 (17%)

Query: 19  DLDEVEFIYKITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDY 77
           DLD       +T+ +L   F+  G V  V++ + +   +   + ++ +     A+ AL+ 
Sbjct: 7   DLDP-----DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 78  FNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKP 137
            N   +    I++              WS+  P S     + NI  K     + + D+K 
Sbjct: 62  MNFKRLGGKPIRI-------------MWSQRDP-SLRRSGVGNIFVK---NLDKSVDNKA 104

Query: 138 GKKSKNDPTFSDFLQLHGKDVS-KLLPLSNKDGEEK-----EEENEDESNNQIAHADISD 191
                   TFS F    G  +S K+   ++++G+ +       E E+      A A I  
Sbjct: 105 LFD-----TFSKF----GNILSCKVA--TDENGKSRGYGFVHFEKEES-----AKAAIQK 148

Query: 192 MEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PL 250
           +  + L  K          +    +     +++  + VKNL   V +  L+  F     +
Sbjct: 149 VNGMLLNDKEVYVGRF---IKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEI 205

Query: 251 ASVRTTFL------GMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAK--YSG 302
            S            G A++ F+  ++  KA+ +         +N  K       K  Y G
Sbjct: 206 TSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE---------MNGKKIGLAKEGKKLYVG 256

Query: 303 AADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGP 362
            A        E  +      QE  ++     A+   ++V+NL  TVT++ L +LF + G 
Sbjct: 257 RAQKRAEREAELRRKFEELQQERKMK-----AQGVNLYVKNLDDTVTDEKLRELFSECGE 311

Query: 363 LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
           +    + +D E   ++GF  V F  PE A +A   + G +  G+ L++   + KE
Sbjct: 312 ITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE 365

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 15/61 (24%), Positives = 31/61 (50%)

Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
           T+E LK  F + G +  +++     G+ + FAF+ +  E+ A+ AL+  N   +    +
Sbjct: 10 TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69

Query: 89 K 89
          +
Sbjct: 70 R 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 55.2 bits (133), Expect = 1e-09
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F++ E S+ + F K G I+ V V + ++ +      S G+GFV F   +    
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQR-----SRGFGFVTFENPDDAKD 57

Query: 643 ALKVLQNSSLDEHQI 657
           A+  +   S+D  QI
Sbjct: 58  AMMAMNGKSVDGRQI 72

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 55.3 bits (134), Expect = 1e-09
 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 9/86 (10%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           T++I+NL F++TE+ ++  F + G +    + + K         S G  FV+F T+ES  
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTG-----HSKGTAFVKFKTKES-- 54

Query: 642 QALKVLQNSSLDEHQIELKRSNRNLE 667
            A K L+ +   E    L    R L 
Sbjct: 55  -AQKCLEAADNAE-DSGLSLDGRRLI 78

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 60.2 bits (146), Expect = 2e-09
 Identities = 43/167 (25%), Positives = 72/167 (43%), Gaps = 19/167 (11%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           +LY+ +L+ + TE  +   FK  GP+ SV V R    +      S+GYG+V F       
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRR-----SLGYGYVNFQNPADAE 56

Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
           +AL+ +    L    I +  S R+         R+S          I V+N+        
Sbjct: 57  RALETMNFKRLGGKPIRIMWSQRD------PSLRRSGV------GNIFVKNLDKSVDNKA 104

Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           + + F  FG +   ++      +G  RG+GFV F  +  AK A++ +
Sbjct: 105 LFDTFSKFGNILSCKV--ATDENGKSRGYGFVHFEKEESAKAAIQKV 149

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 54.5 bits (132), Expect = 2e-09
 Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 2/80 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G+K+ V  +  +  + E+E LF  FG ++ V L K    +G  RGFGFV F +  +A  A
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPE-TGESRGFGFVTFESVEDADAA 59

Query: 745 MKALCQSTHLYGRRLVLEWA 764
           ++ L     L GR + +E A
Sbjct: 60  IRDL-NGKELEGRVIKVEKA 78

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 54.5 bits (132), Expect = 2e-09
 Identities = 24/60 (40%), Positives = 41/60 (68%), Gaps = 1/60 (1%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + +RN+PF A + E++ELF  FGE+K+ R+ K  + +G  +G  FV+F TK  A++ ++A
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKL-TGHSKGTAFVKFKTKESAQKCLEA 61

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 54.5 bits (131), Expect = 2e-09
 Identities = 26/68 (38%), Positives = 37/68 (54%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL   +TED+L K+FE YG + +  L  DK T   +G A V +   E A  A   L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 399 DGTVFLGR 406
           +GT+  G 
Sbjct: 63  NGTIPPGS 70

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V+NL   + ++ L +LF KYG +    +  D +  K+KGF  V F   E A +A + L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 399 DGTVFLGRML 408
           +G    G+ L
Sbjct: 63  NGKEVNGKKL 72

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 23/60 (38%), Positives = 37/60 (61%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  LS   TE DL ++F +YGP+ +V +  D++T +++GF  V F   E A +A + L+G
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 338 RI-FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           RI +VRNL + ++ ++L  LF KYG + ++ +   KE   T+G A V +     A  A  
Sbjct: 3   RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE---TRGTAFVVYEDIYDAKNACD 59

Query: 397 HLDGTVFLGRML 408
           HL G     R L
Sbjct: 60  HLSGFNVANRYL 71

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FV NL   +TE++  +LF KYG ++EV L       K KGF  +      +A +A   
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLDTRTNAEKAKAE 56

Query: 398 LDGTVFLGRML 408
           LDG +  GR L
Sbjct: 57  LDGIMRKGRQL 67

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           T+++ NL+++  ED +R+ F KCG I  V + +    K      S GY +V+F   ES+ 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK------SKGYAYVEFENEESVQ 54

Query: 642 QALK 645
           +ALK
Sbjct: 55  EALK 58

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 23/48 (47%), Positives = 31/48 (64%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           ++FV  L   VTE+DL + F +YG +  V +  DKET K +GFA VTF
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
             T+E+L+  F + G V  V+L    E GK + FAF+ +  E+ A+ AL+  N   +  
Sbjct: 9  PDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDG 68

Query: 86 SRIKV 90
            +KV
Sbjct: 69 RPLKV 73

Length = 73

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ NL+FN TED +R  F+  G I  V +      + P    S GYGF+QF   E   +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQL-----QRDPETGRSKGYGFIQFADAEDAKK 55

Query: 643 ALKVL 647
           AL+ L
Sbjct: 56  ALEQL 60

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 53.8 bits (130), Expect = 5e-09
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV  +     E+D+   F ++G +  + L +D+ T   KG+AL+ +   + A  A + L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 399 DGTVFLGRMLH 409
           +G   LG+ + 
Sbjct: 69  NGKELLGQTIS 79

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 52.8 bits (127), Expect = 6e-09
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +IFV  LS   TEDD+ K F ++G + + +L  DK+T++ +GF  VTF
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 52.6 bits (127), Expect = 7e-09
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT-KGFALVTFLMPEHATQAYQ 396
           ++ VRN+ +  T+ +L +LF  +G +  V LP  K+ D + +GFA V F+  + A  A +
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLP--KKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 397 HLDGTVFLGRMLHLIP 412
            L  T   GR  HL+ 
Sbjct: 60  ALKSTHLYGR--HLVL 73

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 52.8 bits (127), Expect = 7e-09
 Identities = 23/72 (31%), Positives = 42/72 (58%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
            R++V ++S+ + ED + + F  +GP+  + +  D  T K KGFA V + +PE A  A +
Sbjct: 1   CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60

Query: 397 HLDGTVFLGRML 408
            ++G +  GR +
Sbjct: 61  QMNGVMLGGRNI 72

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 52.6 bits (127), Expect = 8e-09
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V  +  +  +  +   F  FG++K +++P     +  HRGF FVEF    +A  A+  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYE-TQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 748 LCQSTHLYGRRL 759
           + +S  L+GR +
Sbjct: 60  MNES-ELFGRTI 70

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 53.0 bits (128), Expect = 8e-09
 Identities = 25/78 (32%), Positives = 43/78 (55%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           +   +S  I++  L Y +TE D+  +F +YG + ++ L  DK+T K+KGFA + +     
Sbjct: 4   DQYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS 63

Query: 391 ATQAYQHLDGTVFLGRML 408
              A  +L+G   LGR +
Sbjct: 64  TILAVDNLNGIKLLGRTI 81

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 52.3 bits (126), Expect = 8e-09
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQA 643
           ++ N+++ +T + ++ HFK CG I  +T+   K    P      G+ +++F  + S+  A
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQP-----KGFAYIEFLDKSSVENA 57

Query: 644 LKVLQNSSLDEHQI 657
           L +L  S     QI
Sbjct: 58  L-LLNESEFRGRQI 70

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 52.6 bits (127), Expect = 9e-09
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 12/85 (14%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y++NL+F   ED +R  F K G + S+ + +K+D K     L+ G+ FV F    S   
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQ--GRLNNGFAFVTFKDASSAEN 60

Query: 643 ALKVLQNSSLDEHQIELKRSNRNLE 667
           AL+      L+  ++      R + 
Sbjct: 61  ALQ------LNGTELG----GRKIS 75

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 52.2 bits (126), Expect = 9e-09
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V NL Y VTE+DL +LF + G + +V +  D+ + +++G A V F   E A +A + 
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 398 LDGTVFLGRMLHL 410
            +G +  G+ + +
Sbjct: 61  FNGVLLDGQPMQV 73

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNEAKRA 744
           ++ VRN+PF   + E+ ELF+AFGE+  V LP  K+   +   +GF FV F+    A +A
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKE---TKRSKGFAFVSFMFPEHAVKA 57

Query: 745 MKAL 748
              L
Sbjct: 58  YSEL 61

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++ NL+F++ EDSI   F + G I+SV +    D   P      G+G+V+F ++E+   
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRP-----KGFGYVEFSSQEAAQA 55

Query: 643 ALKVLQNSSLDEHQIEL 659
           AL  L  + L    + L
Sbjct: 56  ALDALGGTDLLGRPVRL 72

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V N+ F A +  + E F  +GE+  VRLP     SG  +GFG+VEF ++  A+ A+ A
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDP-DSGRPKGFGYVEFSSQEAAQAALDA 59

Query: 748 LCQSTHLYGRRLVLE 762
           L   T L GR + L+
Sbjct: 60  L-GGTDLLGRPVRLD 73

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 57.8 bits (139), Expect = 1e-08
 Identities = 41/153 (26%), Positives = 79/153 (51%), Gaps = 14/153 (9%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
           +Q+   Q  + +A   R++V ++S+ + ED + + F+ +GP+  + +  D  T K KGFA
Sbjct: 93  NQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFA 152

Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQV 441
            V + +PE A  A + ++G +  GR + +  G+P  N            ++  +D   + 
Sbjct: 153 FVEYEVPEAAQLALEQMNGQMLGGRNIKV--GRP-SNMPQ---------AQPIIDMVQE- 199

Query: 442 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 474
            EA+    I V ++      TD+K++FE FG++
Sbjct: 200 -EAKKFNRIYVASVHPDLSETDIKSVFEAFGEI 231

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVIL-----PIDKETDKTKGFALVTFLMPEHATQ 393
           +FV+NL++  TE+ L K FEK G +  V +     P       + G+  V F   E A +
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 394 AYQHLDGTVFLGRMLHL 410
           A + L GTV  G  L L
Sbjct: 63  ALKRLQGTVLDGHALEL 79

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 12/79 (15%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           ILV+N+P     +E+ ELF  FG L  V LP   +          VEF+  +EAK A + 
Sbjct: 3   ILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGIT-------AIVEFLEPSEAKLAFRK 55

Query: 748 L--CQSTHLYGRRLVLEWA 764
           L   +  H+    L LEWA
Sbjct: 56  LAYSKFKHV---PLYLEWA 71

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 28/73 (38%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT-KGFALVTFLMPEHATQAY 395
            +I V+NL +  T+ D+  LF  YG L  V +P  K+ D++ +GFA V F   + A  A 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVP--KKFDQSARGFAFVEFSTAKEALNAM 58

Query: 396 QHLDGTVFLGRML 408
             L  T  LGR L
Sbjct: 59  NALKDTHLLGRRL 71

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 22/70 (31%), Positives = 40/70 (57%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NLS+  TE+ + +LF + G +  +I+ +D+ T    GF  V +   E A  A ++L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 399 DGTVFLGRML 408
           +GT    R++
Sbjct: 61  NGTKLDDRII 70

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +FV NLS++  +DDL + F++ G + +V +  D +  ++KGF  V F   E A +A + 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALE- 58

Query: 398 LDGTVFLGR 406
             G   LGR
Sbjct: 59  KSGEELLGR 67

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV N+ Y  T ++L + F+  G +  + +  DK T + KGFA + FL       A   L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60

Query: 399 DGTVFLGRML 408
           + + F GR +
Sbjct: 61  NESEFRGRQI 70

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 51.9 bits (124), Expect = 2e-08
 Identities = 26/70 (37%), Positives = 41/70 (58%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  LS   TE DL ++F +YGPLA V +  D+ T +++GFA V F   + + +A +H +G
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 401 TVFLGRMLHL 410
               GR + +
Sbjct: 64  MELDGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 17/57 (29%), Positives = 33/57 (57%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++FV  L+   ++  L + F +YG L E ++ +D  T +++GF  +TF   + A +A
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP------IDKETDKTKGFALVTFLMPEHA 391
           R+++ NLSY+ +E+DL +  + + P+  V++P            +  G A   F  PE A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 392 TQAYQHLDGTVFLGRMLHL 410
            +  + L+G VF  R L +
Sbjct: 60  EKVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 22/63 (34%), Positives = 35/63 (55%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RIFV +L   VT++ L + F KY    +  +  DK T K+KG+  V+F  P    +A + 
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

Query: 398 LDG 400
           ++G
Sbjct: 68  MNG 70

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 19/71 (26%), Positives = 31/71 (43%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + V NL    T++   +L   +G +    L   + T ++KG+  V +     A +A   L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 399 DGTVFLGRMLH 409
           DG    GR L 
Sbjct: 62  DGKQIGGRKLQ 72

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L++ +T+DS++ +F + G I    V +  DP +     S G+GFV F +   ++ 
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMK--DPNTKR---SRGFGFVTFASASEVDA 56

Query: 643 ALKVLQNSSLDEHQIELKRS 662
           A+   +   +D  ++E KR+
Sbjct: 57  AMNA-RPHKVDGREVEPKRA 75

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           ILV+N+PF   + E+ ELF+ FG L  + LP         R    VEF+  ++A++A K+
Sbjct: 3   ILVKNLPFGTTEEELRELFEKFGSLGRLLLPPS-------RTIALVEFLEPSDARKAFKS 55

Query: 748 LCQSTHLYGRRLVLEWA 764
           L          L LEWA
Sbjct: 56  LAYK-RFKHVPLYLEWA 71

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 51.0 bits (123), Expect = 3e-08
 Identities = 28/74 (37%), Positives = 42/74 (56%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++FV  L  T TE+D+  LFE+YG + EV +  DK+T ++KG A V F   E A +A + 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 398 LDGTVFLGRMLHLI 411
           L G V +      +
Sbjct: 61  LHGKVTMPGASRPL 74

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 51.3 bits (123), Expect = 3e-08
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           E  ++FV  L ++VT+++L KLF+K+G +  V L  ++ + K KG A V +     A+QA
Sbjct: 1   EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQA 59

Query: 395 YQHLDGTVFLGRML 408
              +DGT    + +
Sbjct: 60  VLKMDGTEIKEKTI 73

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 51.0 bits (123), Expect = 3e-08
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYG--PLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
           + +R L    TE+D+ +        P+ +V L  DK T  ++GFA V F   E ATQ   
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 394 AYQHLDGTVFLGRMLHL 410
           A  +LD  V  GR++ +
Sbjct: 65  ALNNLDPFVIDGRVVRV 81

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IFV N+S T T D+L  LFE++G + E         DK K +A V     E A  A + 
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVEC--------DKVKDYAFVHMEREEEALAAIEA 53

Query: 398 LDGTVFLGRML 408
           L+G    GR +
Sbjct: 54  LNGKEVKGRRI 64

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 8/75 (10%)

Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           S+ L VRNI    +  E+  LF+ FG++      + +  +  HRGF  V +     A+RA
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDI------RTLYTACKHRGFIMVSYYDIRAARRA 54

Query: 745 MKALCQSTHLYGRRL 759
            +AL Q T L GR+L
Sbjct: 55  KRAL-QGTELGGRKL 68

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 56.1 bits (135), Expect = 4e-08
 Identities = 45/171 (26%), Positives = 74/171 (43%), Gaps = 20/171 (11%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  L+    E DL + F K G + +V    D+ + ++KG A V F   E   +A   L
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-L 150

Query: 399 DGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYR 458
            G + LGR + +   +  + E N   K           A +Q  +  +   + V NL + 
Sbjct: 151 TGQMLLGRPIIV---QSSQAEKNRAAKA----------ATHQPGDIPNFLKLYVGNLHFN 197

Query: 459 TLPTDLKALFEPFGDLGRVLVP--PYGIT----GLVEFLQKNQAKAAFNSL 503
               +L+ +FEPFGD+  V +   P        G ++F    +AK A   +
Sbjct: 198 ITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 51.1 bits (123), Expect = 4e-08
 Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 7/82 (8%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEV-IL-PIDKETDKTK---GFALVTFLMPEHATQ 393
           ++V NL+  VTE+ L + F ++GPLA V I+ P  +E  +     GF  V F+    A +
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGF--VAFMNRADAER 61

Query: 394 AYQHLDGTVFLGRMLHLIPGKP 415
           A   LDG   +G  L L  GK 
Sbjct: 62  ALDELDGKDVMGYELKLGWGKA 83

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 6/70 (8%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL + +TE++L + F  +G + EV         K KG+A V F   E A  A   +
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEV------RVFKDKGYAFVRFDTHEAAATAIVAV 56

Query: 399 DGTVFLGRML 408
           +GT   G+ +
Sbjct: 57  NGTSINGQTV 66

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 50.5 bits (121), Expect = 4e-08
 Identities = 28/69 (40%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +++ NL++ +TEDD+ + F K   +  V L  DKET + KGF  V F   E +  A   
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDF-ADEESLDAALK 58

Query: 398 LDGTVFLGR 406
           LDGTV  GR
Sbjct: 59  LDGTVLCGR 67

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 50.4 bits (121), Expect = 5e-08
 Identities = 17/60 (28%), Positives = 31/60 (51%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  L   +T+++L  LFE  GP+    +  D+ T ++ G+  V ++    A +A   L+G
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 50.3 bits (121), Expect = 6e-08
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRN++  V +++L  LFE++G +  +         K +GF +V++     A +A + L
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLYTAC-----KHRGFIMVSYYDIRAARRAKRAL 58

Query: 399 DGTVFLGRMLHLIPGKPKE 417
            GT   GR L +    PK+
Sbjct: 59  QGTELGGRKLDIHFSIPKD 77

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 49.9 bits (120), Expect = 7e-08
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           TT+Y+ NL    TE+ ++R F   G I  V V + K           GY FV+F T E+ 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-----------GYAFVRFDTHEAA 49

Query: 641 NQALKVLQNSSLDEHQI 657
             A+  +  +S++   +
Sbjct: 50  ATAIVAVNGTSINGQTV 66

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 50.0 bits (120), Expect = 7e-08
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 4/69 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE---HATQA 394
           ++FV NL +TV   +L + F ++G +    +P DKET  +KG+  V+F   +   +A Q 
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 395 YQH-LDGTV 402
            +H L+G  
Sbjct: 61  QKHILEGNK 69

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 49.7 bits (119), Expect = 7e-08
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV NL Y V    L ++F+  G +    +  DKE  K++G  +V F  P  A QA    
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 399 DGTVFLGRMLHL 410
           +G +   R + +
Sbjct: 60  NGQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 50.0 bits (120), Expect = 8e-08
 Identities = 26/70 (37%), Positives = 34/70 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV NL     E  L +LF  +G +  V +  D  T+K KG+  VT    E A  A   L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 399 DGTVFLGRML 408
           +G    GR+L
Sbjct: 64  NGYRLGGRVL 73

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 50.0 bits (119), Expect = 8e-08
 Identities = 25/70 (35%), Positives = 42/70 (60%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A +  +G
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 401 TVFLGRMLHL 410
               GR + +
Sbjct: 74  MELDGRRIRV 83

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 50.0 bits (119), Expect = 9e-08
 Identities = 25/72 (34%), Positives = 40/72 (55%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRN++     +DL + F +YGP+ +V +P+D  T + +GFA V F     A  A  +L
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 399 DGTVFLGRMLHL 410
           D     GR + +
Sbjct: 63  DRKWICGRQIEI 74

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-------GLVEFLQKNQAKAAFNS 502
           ILV+N+P+     +L+ LF  FG+L  V +P            G V+F+ K  AK AF +
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 503 LAY-TKFKEVPLYLEWA 518
           L + T      L LEWA
Sbjct: 63  LCHSTHLYGRRLVLEWA 79

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 49.6 bits (119), Expect = 1e-07
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV--ARKKDPKSPGQFLSMGYGFVQFYTRE 638
           T LY+ NLN   TE+ + + F + GP+ASV +   R ++ +   +      GFV F  R 
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC----GFVAFMNRA 57

Query: 639 SLNQALKVLQNSSLDEHQIEL 659
              +AL  L    +  ++++L
Sbjct: 58  DAERALDELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 20/83 (24%), Positives = 46/83 (55%), Gaps = 4/83 (4%)

Query: 687 KILVRNIPFQAKQSE-VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           K+++RN+P+  K+   ++++F  +G+++   +P+K    G   GF FV    +  A+ A+
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRK--RGGKLCGFAFVTMKKRKNAEIAL 59

Query: 746 KALCQSTHLYGRRLVLEWAEEAD 768
           +       + GR + ++WA + +
Sbjct: 60  ENT-NGLEIDGRPVAVDWAVQKN 81

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 25/70 (35%), Positives = 37/70 (52%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV N+ Y  TE+ L  +F + GP+    L  D+ET K KG+    +   E A  A ++L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 399 DGTVFLGRML 408
           +G    GR L
Sbjct: 61  NGYELNGRQL 70

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 53.4 bits (127), Expect = 2e-07
 Identities = 39/156 (25%), Positives = 68/156 (43%), Gaps = 7/156 (4%)

Query: 614 RKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTV 673
                K   +        +    R+  N+     QN     +  E +          ++ 
Sbjct: 49  EVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFR-----SSE 103

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
             KS   +K+  + + V N+P+   + ++ ELFK FG +K VRL +    +G  RGF FV
Sbjct: 104 SPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRE-TGKSRGFAFV 162

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
           EF ++  A++A++ L     L GR L ++ A+ A  
Sbjct: 163 EFESEESAEKAIEEL-NGKELEGRPLRVQKAQPASQ 197

Length = 306

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 12/83 (14%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           I V N+   A + ++ ELF+ FG +  V L K    +G  RGF FV F T+ +A+RA++ 
Sbjct: 2   IRVTNLSEDADEDDLRELFRPFGPISRVYLAKDK-ETGQSRGFAFVTFHTREDAERAIE- 59

Query: 748 LCQSTHLYGRR---LVL--EWAE 765
                 L G     L+L  EWA+
Sbjct: 60  -----KLNGFGYDNLILSVEWAK 77

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L + NL + +T D +RR F+K G +  V +     P+      S G+ FV+FY +     
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYI-----PRDRYTRESRGFAFVRFYDKRDAED 55

Query: 643 ALKVLQNSSLD 653
           A+  +    LD
Sbjct: 56  AMDAMDGKELD 66

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 24/60 (40%), Positives = 32/60 (53%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L    T + L  +F KYG +  V LP  K T   KGFA + F  PE A +A +HL
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           +P  TL++  L+  +TE+++R  F + G I  + + R       G   S GY FV++   
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRD---IVTGF--SKGYAFVEYEHE 55

Query: 638 ESLNQALKVLQNSSLDEHQI 657
               +A +      +D  +I
Sbjct: 56  RDALRAYRDAHKLVIDGSEI 75

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
           P+  L++  LN  +T++ +   F + G I S  V R  D K+ G   S+ Y F++F T+E
Sbjct: 2   PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIR--DKKT-GD--SLQYAFIEFETKE 56

Query: 639 SLNQALKVLQNSSLDEHQI 657
              +A   + N  +D+ +I
Sbjct: 57  DCEEAYFKMDNVLIDDRRI 75

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGP---LAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           R+++ NL   +TE  L KLF KYG       +         + +G+  VTF   E A +A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 395 YQHLDGTVFLGRML 408
            + L+G   LG+ L
Sbjct: 61  LKSLNGKTALGKKL 74

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 28/67 (41%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           T+YI NL ++ TED +R  F K   I SV +A  K+    G+F   G+G V F   ESL+
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKE---TGEF--KGFGHVDFADEESLD 54

Query: 642 QALKVLQ 648
            ALK+  
Sbjct: 55  AALKLDG 61

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 21/60 (35%), Positives = 31/60 (51%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IFV  L   VTE DL K F ++G + EV++  D E  + +GF  +TF   +   Q    
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            L++ NL +++T + +  HFK  G   SV +   K           G  FV+F T E++ 
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKS-----KGCAFVEFDTAEAMT 56

Query: 642 QALKVLQNSSLDEHQI 657
           +ALK L ++ L   +I
Sbjct: 57  KALK-LHHTLLKGRKI 71

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+++NL F +TE+ +R  F+  G I+ V +   K+ K      S G+ FV F   E   +
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKR-----SKGFAFVSFMFPEHAVK 56

Query: 643 ALKVLQNSSLD 653
           A   L  S   
Sbjct: 57  AYSELDGSIFQ 67

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 7/77 (9%)

Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNE 740
           +TG ++ VRN+P+  K+ ++E+LF  FGEL  V +   KK   SG  +GF +V F+   +
Sbjct: 1   ETG-RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKK---SGKSKGFAYVLFLDPED 56

Query: 741 AKRAMKALCQSTHLYGR 757
           A +A K L       GR
Sbjct: 57  AVKAYKEL-DGKVFQGR 72

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 48.4 bits (116), Expect = 4e-07
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL++  LN+++TE  +RR F++ GPI  + + R K    P      GY F++F     + 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKP-----RGYAFIEFEHERDMK 57

Query: 642 QALK 645
            A K
Sbjct: 58  AAYK 61

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL Y+V ED+L KLF K G + +V L  + +  K+KG+A V F   E   +A + L
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKG-KSKGYAYVEFENEESVQEALK-L 59

Query: 399 DGTVFLGR 406
           D  +  GR
Sbjct: 60  DRELIKGR 67

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 47.9 bits (115), Expect = 4e-07
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCG--PIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
           P  TL ++ L+  +TE+ I +        PI  V + R  D  +     S G+ FV+F +
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIR--DKLTG---TSRGFAFVEFPS 55

Query: 637 RESLNQALKVLQNS 650
            E   Q +  L N 
Sbjct: 56  LEDATQWMDALNNL 69

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 48.1 bits (115), Expect = 4e-07
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V  +P  A    ++ +F  +G + +V LP+    +G  +GF F+EF T  EA++A K 
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPR-YKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 748 LCQS 751
           L   
Sbjct: 61  LNNP 64

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH- 397
           +F+  LS+  TE+ L + F KYG + + ++  D  T +++GF  VTF  P    +     
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 398 ---LDG 400
              LDG
Sbjct: 61  PHVLDG 66

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            LY+ NL +N TE+ ++  F + G + S  V   ++        S G+GFV+  T E  N
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGR-----SRGFGFVEMETAEEAN 55

Query: 642 QALKVLQNSSLDEHQI 657
            A++ L  +      +
Sbjct: 56  AAIEKLNGTDFGGRTL 71

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           +KI V  +P+      + + F  FGE++   V   ++   +G  RG+GFV F  K  A+R
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQ---TGKSRGYGFVTFKDKESAER 57

Query: 744 AMKALCQSTHLYGRRLVLEWA 764
           A K    +  + GR+  +  A
Sbjct: 58  ACKDP--NPIIDGRKANVNLA 76

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 47.5 bits (113), Expect = 5e-07
 Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 6/80 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++  LN  +++  +RRHF + G +    V    + K      S G+GF+ F + +  ++
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTK-----RSRGFGFITFSSADEADE 59

Query: 643 ALKVLQNSSLDEHQIELKRS 662
           A++  Q  S+D +QIELKR+
Sbjct: 60  AMEA-QPHSIDGNQIELKRA 78

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 47.7 bits (114), Expect = 5e-07
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 5/84 (5%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           T+Y++ L  N+T + ++  F K G +  V++ R K           G+ F++F T E   
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDI-----KGFAFIEFETPEEAQ 55

Query: 642 QALKVLQNSSLDEHQIELKRSNRN 665
           +A K L N          K     
Sbjct: 56  KACKHLNNPPETATDKPGKFPKTV 79

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 28/68 (41%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL Y  T +DL   F+  G    V L  DK+T K+KG A V F   E  T+A + L
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-L 61

Query: 399 DGTVFLGR 406
             T+  GR
Sbjct: 62  HHTLLKGR 69

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RI+V ++   ++EDD+  +FE +G +    L  D ET K KG+  + +  P+ A  A   
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 398 LDGTVFLGRMLH 409
           ++     G+ L 
Sbjct: 62  MNLFDLGGQQLR 73

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 47.7 bits (114), Expect = 5e-07
 Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           V  +P    Q E+E LF  +G +   R+    V  GL RG GF+ F  + EA+RA+KAL
Sbjct: 5   VSGLPKTMTQQELEALFSPYGRIITSRILCDNVT-GLSRGVGFIRFDKRIEAERAIKAL 62

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V+NL  ++ ++ L + F  +G +    +  D E  ++KGF  V F  PE AT+A   +
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 399 DGTVFLGRMLHLIPGKP 415
           +G         +I GKP
Sbjct: 63  NG--------RIIGGKP 71

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 47.3 bits (113), Expect = 6e-07
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 2/66 (3%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S+++V+N+P   K+ ++ +LF+AFG +  V+L  K    G  R FGFV + T+ EA++A+
Sbjct: 1   SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQL--KYTKDGKFRKFGFVGYKTEEEAQKAL 58

Query: 746 KALCQS 751
           K    S
Sbjct: 59  KHFNNS 64

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 47.4 bits (113), Expect = 6e-07
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V N+ +   + DL ++F ++GP+ +V   I      +KGF  VTF     A +A + 
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDV--EIIFNERGSKGFGFVTFANSADADRAREK 59

Query: 398 LDGTVFLGRML 408
           L GTV  GR +
Sbjct: 60  LHGTVVEGRKI 70

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 47.2 bits (113), Expect = 7e-07
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNSLA 504
           ++V+N+P+     +L+ LF PFG +  V +P    G       VEF+ K +A+ A  +L 
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62

Query: 505 YTKFKEVPLYLEWA 518
            T      L LE+A
Sbjct: 63  STHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          + IT++ L+  FE  G +  VQL+   E G+ + + FI +   + A+ AL+  N   +  
Sbjct: 8  FNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAG 67

Query: 86 SRIKV 90
            IKV
Sbjct: 68 RPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 47.4 bits (113), Expect = 7e-07
 Identities = 26/80 (32%), Positives = 39/80 (48%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++FV  +   + E DL  LFE++G + E+ +  DK T   KG A +T+   E A +A   
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 398 LDGTVFLGRMLHLIPGKPKE 417
           L     L  M   I  KP +
Sbjct: 67  LHEQKTLPGMNRPIQVKPAD 86

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 46.9 bits (112), Expect = 8e-07
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L ++NL F  TE  +++ F   G +  VT+ RK D K        G+ FVQF ++    +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGK------KKGFAFVQFTSKADAEK 55

Query: 643 ALKVLQNSSLDEHQI 657
           A+K +    +    +
Sbjct: 56  AIKGVNGKKIKGRPV 70

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 47.2 bits (113), Expect = 8e-07
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T +Y+KNL  +  ++ ++  F K G I S  V +  + K      S G+GFV F   E+ 
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGK------SKGFGFVNFENHEAA 55

Query: 641 NQALKVLQNSSLDEHQI 657
            +A++ L    ++  ++
Sbjct: 56  QKAVEELNGKEVNGKKL 72

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 46.8 bits (111), Expect = 8e-07
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V N+P    +S +  LF+ +G+++ V+         +  G   V F    +AKRA++ 
Sbjct: 4   LFVINVPRDVTESTLRRLFEVYGDVRGVQT------ERISEGIVTVHFYDIRDAKRAVRE 57

Query: 748 LCQSTHLYGRRL 759
           LC   H+  + L
Sbjct: 58  LC-GRHMQQQAL 68

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 46.5 bits (111), Expect = 8e-07
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 11/75 (14%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHATQA 394
            R+ V NL  +VTEDD+ +LF   G L  A ++ P         G A V ++  + A  A
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRP---------GVAEVVYVRKDDALTA 51

Query: 395 YQHLDGTVFLGRMLH 409
               +     G+ + 
Sbjct: 52  IDKYNNRELDGQPMK 66

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 46.4 bits (111), Expect = 8e-07
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 5/58 (8%)

Query: 353 LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL 410
           L KLF  +G + ++ L   K      GFA V F   E A +A Q+L+G +F GR L +
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 46.8 bits (112), Expect = 9e-07
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  +   + ED+L  LFEK GP+ E+ L +D      +G+A VT+   E A +A + L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSG-LNRGYAFVTYTNKEAAQRAVKQL 62

Query: 399 DG 400
             
Sbjct: 63  HN 64

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V+NL   + ED L KLFE +G + +V L   K+  K + F  V +   E A +A +H
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKH 60

Query: 398 LDGTVF 403
            + +  
Sbjct: 61  FNNSFI 66

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 51.1 bits (121), Expect = 1e-06
 Identities = 44/230 (19%), Positives = 86/230 (37%), Gaps = 26/230 (11%)

Query: 165 SNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQY 224
            +K      E  E+         D       + + +   ++ S  S          K + 
Sbjct: 62  PSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQK------SKEEN 115

Query: 225 HTIVVKNLPAGVKKKDLKAYFKP--------LPLASVRTTFLGMAYIGFKDEKNCNKALN 276
           +T+ V NLP  V ++DL+  FK         L          G A++ F+ E++  KA+ 
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 277 K-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAE 335
           + N    +G+ L + K    +  +   + + + + + +  + K           A  + +
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGK-----------ALLLEK 224

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           S  ++V NL     E++L  LF+  G +    LP  K+    K  + V  
Sbjct: 225 SDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN 274

Length = 306

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 47.6 bits (113), Expect = 1e-06
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPI--ASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           D TL+++NL +++TE+S+  HF K G +  A   + +           + G GFV F  +
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTG-------RAKGTGFVCFKDQ 53

Query: 638 ESLNQALK 645
            + N  LK
Sbjct: 54  YTYNACLK 61

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 51.6 bits (123), Expect = 1e-06
 Identities = 40/168 (23%), Positives = 81/168 (48%), Gaps = 13/168 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y+ +++F   ED+IRR F   GPI S+ ++   DP +       G+ FV++   E+   
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSW--DPATGKH---KGFAFVEYEVPEAAQL 164

Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGS--KILVRNIPFQAKQS 700
           AL+ +    L    I++        S     +     V ++     +I V ++     ++
Sbjct: 165 ALEQMNGQMLGGRNIKV-----GRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSET 219

Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           +++ +F+AFGE+   +L +   G G H+G+GF+E+        A+ ++
Sbjct: 220 DIKSVFEAFGEIVKCQLARAPTGRG-HKGYGFIEYNNLQSQSEAIASM 266

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           ++ V NIPF+ +  ++ ++F  FG +  V +     GS   +GFGFV F    +A RA +
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS---KGFGFVTFANSADADRARE 58

Query: 747 ALCQSTHLYGRRL 759
            L   T + GR++
Sbjct: 59  KL-HGTVVEGRKI 70

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G ++ V  IP    + E+  LF+  G +  +RL   M  SGL+RG+ FV +  K  A+RA
Sbjct: 1   GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRL--MMDFSGLNRGYAFVTYTNKEAAQRA 58

Query: 745 MKAL 748
           +K L
Sbjct: 59  VKQL 62

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV  LS  VT+++L + F ++G + EV L   K  + T  FA + F   + A +A +  
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 399 DGTVFLGRMLH 409
           + ++   + +H
Sbjct: 64  NHSMLKNKTMH 74

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 22/71 (30%), Positives = 34/71 (47%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IF+  L   ++ED + +L E +G L    L  D  T  +KG+A   +L P    QA   
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 398 LDGTVFLGRML 408
           L+G     + L
Sbjct: 62  LNGMQLGDKKL 72

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 22/70 (31%), Positives = 33/70 (47%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  LS T    DL +LF KYG +    +  +  +   + F  VT    E A +  QHL
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 399 DGTVFLGRML 408
             T   GR++
Sbjct: 62  HRTELHGRVI 71

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 23/70 (32%), Positives = 38/70 (54%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL   VTE+ L +LF + GP+  V +P D+ T   +G+  V FL  E A  A + +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 399 DGTVFLGRML 408
           +     G+ +
Sbjct: 61  NMIKLYGKPI 70

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           ILV+N P+     E+ +LF+  G+L  V +P     +G       VEF    +A+ A KA
Sbjct: 3   ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPP----AGT---IAIVEFANPQQARLAFKA 55

Query: 748 LCQSTHLYGRRLVLEWA 764
           L          L LE  
Sbjct: 56  LAY-RRFKDSILYLEKG 71

This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + VRN+    +  ++  LF  +G +  V +P     +   RGF +V+F    +A+ A+
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFY-TRRPRGFAYVQFEDVRDAEDAL 59

Query: 746 KALCQSTHLYGRRLVLEWAE 765
             L   T   GR + +++A+
Sbjct: 60  YYL-DRTRFLGREIEIQFAQ 78

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          Y +T+E LK  F + G VT  ++    E G+ R F F+     ++A AA++  N T    
Sbjct: 9  YNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGG 68

Query: 86 SRIKV 90
            + V
Sbjct: 69 RTLTV 73

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           T+ + NL+ ++ ED +R  F+  GPI+ V +A+ K+        S G+ FV F+TRE   
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETG-----QSRGFAFVTFHTREDAE 55

Query: 642 QALKVLQNSSLD 653
           +A++ L     D
Sbjct: 56  RAIEKLNGFGYD 67

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL+++NL F+ T++ +   F    PI    V    DP++ G+  S GYGFV F   E   
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVV--TDPET-GE--SRGYGFVTFAMLEDAQ 55

Query: 642 QALKVLQNSSLDEHQIEL 659
           +AL  L+N  L    + L
Sbjct: 56  EALAKLKNKKLHGRILRL 73

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           + V N+ +   + E+ +LF   GE+  VRL K   G    +G+ +VEF  +   + A+K
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK--SKGYAYVEFENEESVQEALK 58

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 16/48 (33%), Positives = 29/48 (60%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           ++F+  LSY  T+D L   F ++G + + ++  D  T +++GF  VTF
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTF 48

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 6/78 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L++++TE+S+R +F K G +    +   KDP + G+  S G+GFV F    S+++
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVI--MKDPIT-GR--SRGFGFVTFADPSSVDK 55

Query: 643 ALKVLQNSSLDEHQIELK 660
            L   +   LD  +I+ K
Sbjct: 56  VLA-AKPHVLDGREIDPK 72

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 30/73 (41%), Positives = 40/73 (54%), Gaps = 7/73 (9%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD---KTKGFALVTFLMPEHATQAY 395
           IFVRNL ++VT  DL  LF + G     +L  D +TD   ++KGF  V F  PE A +A 
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGN----VLRADVKTDNDGRSKGFGTVLFESPEDAQRAI 56

Query: 396 QHLDGTVFLGRML 408
           +  +G    GR L
Sbjct: 57  EMFNGYDLEGREL 69

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 22/68 (32%), Positives = 37/68 (54%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV +LS  +  + L   F  +G +++  +  D +T K+KG+  V+F+  E A  A Q +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 399 DGTVFLGR 406
           +G    GR
Sbjct: 62  NGQWLGGR 69

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 4/67 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP---EHATQA 394
           ++FV  LS+  T++ L + F +YG + + ++  DK T++++GF  V F  P         
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 395 YQH-LDG 400
             H LDG
Sbjct: 61  GPHTLDG 67

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 21/48 (43%), Positives = 33/48 (68%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +IFV  LS   TE+ + + F K+G + E+ LP+DK+T+K +GF  +TF
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF 48

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 23/56 (41%), Positives = 32/56 (57%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +FV NLS+  TED+L   F + G +  V +   +++ K KGFA V F   E AT A
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA 56

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
           + V NLP  T   +L+ LF  FG +  V +     TG       VEF  +  A+ A  +L
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 504 AYTKFKEVPLYL 515
              +    PL +
Sbjct: 62  NGKELDGRPLKV 73

Length = 73

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 45.5 bits (108), Expect = 3e-06
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ V  +PF   + E+E+LFK  G +K VRL      SG  +G  +VE+  ++ A +A+ 
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR--SGKPKGLAYVEYENESSASQAVL 61

Query: 747 AL 748
            +
Sbjct: 62  KM 63

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 45.6 bits (109), Expect = 3e-06
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           + +++R +     + ++ +   A   +    VRL +  + +G  RGF FVEF +  +A +
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKL-TGTSRGFAFVEFPSLEDATQ 61

Query: 744 AMKALCQSTHLY--GRRLVLEWA 764
            M AL         GR + + +A
Sbjct: 62  WMDALNNLDPFVIDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+KNL+ +  ++ +R  F   G I S  V    D K  G+  S G+GFV F + E   +
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMT--DEK--GR--SKGFGFVCFSSPEEATK 57

Query: 643 ALK 645
           A+ 
Sbjct: 58  AVT 60

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 25/69 (36%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +++V NL    T+ +L   FEKYGPL  V +          GFA V F  P  A  A + 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRA 55

Query: 398 LDGTVFLGR 406
           LDG    G 
Sbjct: 56  LDGRRICGN 64

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 23/72 (31%), Positives = 40/72 (55%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRN++     +DL + F +YGP+ +V +P+D  T + +GFA + F     A  A  +L
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 399 DGTVFLGRMLHL 410
           +     GR + +
Sbjct: 63  NRKWVCGRQIEI 74

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FV NL   +TE+++ KLFEKYG   E+ +       K KGF  +       A  A   
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFI------HKDKGFGFIRLETRTLAEIAKAE 56

Query: 398 LDGTVFLGRMLHL 410
           LD     G+ L +
Sbjct: 57  LDNMPLRGKQLRV 69

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V N+  +  +  + ELF   G +  V +PK  V +  H+G+GFVEF+++ +A  A+K 
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRV-TQAHQGYGFVEFLSEEDADYAIKI 59

Query: 748 LCQSTHLYGR 757
           +     LYG+
Sbjct: 60  M-NMIKLYGK 68

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++ NL+F +TED +R HF + G I  V +   +D          G+ FV F   E    
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGK-----CKGFAFVDFEEIEFATN 55

Query: 643 ALK 645
           ALK
Sbjct: 56  ALK 58

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 45.3 bits (108), Expect = 4e-06
 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 7/88 (7%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           TT+++ N+    ++D IR+  +KCG + S    R KDP + G+     +GF +F   E  
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWK--RVKDPST-GKLK--AFGFCEFEDPEGA 55

Query: 641 NQALKVLQNSSLDEHQIELK--RSNRNL 666
            +AL++L    L   ++ +K     R L
Sbjct: 56  LRALRLLNGLELGGKKLLVKVDAKTRKL 83

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           T Y+ NL ++ TE+ I+  F+    ++SV + R  +P  PG+    G+G+ +F  R+SL 
Sbjct: 3   TAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPR--EPGDPGRL--RGFGYAEFEDRDSLL 57

Query: 642 QALKVLQNSSLDEHQI 657
           QAL  L + SL   +I
Sbjct: 58  QALS-LNDESLKNRRI 72

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 44.8 bits (107), Expect = 4e-06
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ +L+ + TE  +   F   GP+ S+ V R  D  +     S+GY +V F       +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCR--DLITRR---SLGYAYVNFQNPADAER 56

Query: 643 ALKVLQNSSLDEHQIELKRSNRN 665
           AL  L    +    I +  S R+
Sbjct: 57  ALDTLNFDVIKGKPIRIMWSQRD 79

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           + + +KNL    TED +R HF+  G +  V V R +D KS  +F     GFV F + E  
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSR-RF-----GFVGFKSEEDA 54

Query: 641 NQALKVLQNSSLDEHQIE 658
            QA+K    + +D  +I 
Sbjct: 55  QQAVKYFNKTFIDTSKIS 72

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 44.9 bits (107), Expect = 5e-06
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 28 KITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          + T+++L+A F + G V +V L K    G+ R F F+ +   + A AA+   N   +   
Sbjct: 12 RTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGR 71

Query: 87 RIKVEK 92
           IKVEK
Sbjct: 72 VIKVEK 77

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 44.4 bits (105), Expect = 5e-06
 Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 9/79 (11%)

Query: 338 RIFVRNL-SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           R+F+ NL +  V+++DL ++F  YG LA+++L           +  V F  PE    A  
Sbjct: 1   RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAIN 52

Query: 397 HLDGTVFLGRMLHLIPGKP 415
              G +  GR LHL   KP
Sbjct: 53  CEQGKMIRGRKLHLEVSKP 71

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
           V N+ ++    ++  +F+ +GE+  V +P+    +   RGF FV F  K +A+ AM A+ 
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDR-YTRESRGFAFVRFYDKRDAEDAMDAM- 60

Query: 750 QSTHLYGRRL 759
               L GR L
Sbjct: 61  DGKELDGREL 70

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 5/65 (7%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T +++  L +++T+DS+R++F + G I    V    D +  G+  S GYGFV F  +ES 
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVV--ITD-RQTGK--SRGYGFVTFKDKESA 55

Query: 641 NQALK 645
            +A K
Sbjct: 56  ERACK 60

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 7/61 (11%)

Query: 689 LVRNIPFQAKQSEVEELFKAFGELKFVRLP-KKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           L RN+     +  ++E+F  +G +K V LP  + V   L RG+ +VEF +  +A++A+K 
Sbjct: 6   LTRNV----NKDHLKEIFSNYGTVKDVDLPIDREVN--LPRGYAYVEFESPEDAEKAIKH 59

Query: 748 L 748
           +
Sbjct: 60  M 60

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 44.6 bits (106), Expect = 6e-06
 Identities = 16/62 (25%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           +I V ++     + +++ +F+AFG++K   L      +G H+G+GF+E+     A+ A+ 
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPE-TGKHKGYGFIEYENPQSAQDAIA 60

Query: 747 AL 748
           ++
Sbjct: 61  SM 62

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 5/84 (5%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
             L++  L+  +TE  +   F K G +  V +   KDP++ G+  S G+GFV F + E  
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLM--KDPET-GE--SRGFGFVTFESVEDA 56

Query: 641 NQALKVLQNSSLDEHQIELKRSNR 664
           + A++ L    L+   I+++++ R
Sbjct: 57  DAAIRDLNGKELEGRVIKVEKAKR 80

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 19/59 (32%), Positives = 38/59 (64%), Gaps = 1/59 (1%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           V N+ F   + ++  +F+ FGE++FV+L +    +G  +G+GF++F    +AK+A++ L
Sbjct: 3   VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDP-ETGRSKGYGFIQFADAEDAKKALEQL 60

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL + + E++L K FE  G +  V +  D++T   KGF  V F   +    A + L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-L 60

Query: 399 DGTVFLGR 406
           +G    GR
Sbjct: 61  NGIKLKGR 68

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL  TVTED L +LF + GP+    L  +   D    +A V +     A  A Q +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP---YAFVEYYDHRSAAAALQTM 57

Query: 399 DGTVFLGR 406
           +G + LG+
Sbjct: 58  NGRLILGQ 65

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 46.2 bits (109), Expect = 7e-06
 Identities = 22/77 (28%), Positives = 39/77 (50%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S ++F+  LS+   +  L   F  +G + +  + +D+ET +++GF  V F     AT A 
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 396 QHLDGTVFLGRMLHLIP 412
             +DG    GR + + P
Sbjct: 94  SEMDGKELNGRHIRVNP 110

Length = 144

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  LS  V E DL + F K G + +V +  D+ + ++KG A V F   E    A   L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-L 60

Query: 399 DGTVFLG 405
            G   LG
Sbjct: 61  TGQRLLG 67

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 44.5 bits (105), Expect = 7e-06
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++ NL F   E+ + R F KCG I  V + R  DPK+    +  G+ +VQF    ++ +
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVR--DPKTN---VGKGFAYVQFKDENAVEK 56

Query: 643 AL 644
           AL
Sbjct: 57  AL 58

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 44.3 bits (104), Expect = 8e-06
 Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 6/80 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T+DS+R HF+K G +    V R  DP++     S G+GFV +   E ++ 
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMR--DPQTK---RSRGFGFVTYSCVEEVDA 59

Query: 643 ALKVLQNSSLDEHQIELKRS 662
           A+   +   +D   +E KR+
Sbjct: 60  AM-SARPHKVDGRVVEPKRA 78

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 43.7 bits (104), Expect = 9e-06
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 9/73 (12%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR-------TTFLGMAYIGFKDEKNCNKALNK 277
           T+ V NLP    +++L+  F     + SVR           G A++ F+ E++  KAL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 278 -NKSFWKGKQLNI 289
            N     G+ L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 43.9 bits (104), Expect = 9e-06
 Identities = 27/69 (39%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
           FV NL +   + DL  +F+    +  V L  DKETDK KGF  V F   E   +A +  D
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 400 GTVFLGRML 408
           G +F  R L
Sbjct: 63  GALFDDRSL 71

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 5/72 (6%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 504
           + V NLP  T   DL+ LF  FG++  V +             VEF     A+ A  +L 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 505 YTKFKEVPLYLE 516
             +     L + 
Sbjct: 61  GKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 47.6 bits (112), Expect = 1e-05
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYT-TEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           Y +T+E L+  F++ G V  V+L      GK R FAF+ +  E+ A+ A++  N   +  
Sbjct: 125 YDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEG 184

Query: 86  SRIKVEKCSNLGDTTKPKS 104
             ++V+K           S
Sbjct: 185 RPLRVQKAQPASQPRSELS 203

Length = 306

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V NIP+ A + ++ E+F   G +   RL      +G  +G+GF EF     A  A++ 
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRD-TGKPKGYGFCEFEDIETAASAIRN 59

Query: 748 LCQSTHLYGRRLVLEWA 764
           L       GR L +++A
Sbjct: 60  L-NGYEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 21/64 (32%), Positives = 33/64 (51%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  LS   TE+ L ++F +YG +  + L  D  T  +KG+A V +     A +AY+  
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 399 DGTV 402
              V
Sbjct: 66  HKLV 69

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 43.6 bits (102), Expect = 1e-05
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++F+  LS+  T+D L + FEK+G L + ++  D +T +++GF  VT+   E    A
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++VRNL  + TE+ L +LF +YG +  V    D        +A V F   + A +A + +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 399 DGTVFLGRMLHLIPGKP 415
           +G    G  + +   KP
Sbjct: 56  NGKELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 8/73 (10%)

Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
           L   + E  +   F + G +  V +  +K+T K+ G+  V F   E A QA Q L+G   
Sbjct: 7   LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGK-- 64

Query: 404 LGRMLHLIPGKPK 416
                  IP   +
Sbjct: 65  ------PIPNTQQ 71

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 11/70 (15%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           TTLY+  L    TE  +R HF + G I S+TV  ++              FV F TRE+ 
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQ-----------QCAFVTFTTREAA 50

Query: 641 NQALKVLQNS 650
            +A + L N 
Sbjct: 51  EKAAERLFNK 60

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FV NL   +TE+D  KLFEKYG  +EV +      ++ +GF  +       A  A   
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 56

Query: 398 LDGTVFLGRMLHL 410
           LDGT+   R L +
Sbjct: 57  LDGTILKNRPLRI 69

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 8/83 (9%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           ++Y+ N+++ ST + +  HF  CGPI  VT+   K    P      GY +++F TR+S+ 
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHP-----KGYAYIEFATRDSVE 55

Query: 642 QALKVLQNSSLDEHQIEL--KRS 662
            A+  L  SS     I++  KR+
Sbjct: 56  AAVA-LDESSFRGRVIKVLPKRT 77

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V N+ Y  T ++L   F   GP+  V +  DK +   KG+A + F     + +A   L
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAVAL 60

Query: 399 DGTVFLGRMLHLIP 412
           D + F GR++ ++P
Sbjct: 61  DESSFRGRVIKVLP 74

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 27/71 (38%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RI+V NL   + E D+  LF KYGP+  + L   K   +   FA V F  P  A  A + 
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRG 57

Query: 398 LDGTVFLGRML 408
            DG  F G  L
Sbjct: 58  RDGYDFDGYRL 68

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FV  +  + TE+DL + F+++G +  V +  DK T ++KGF  V F  P  A  A ++
Sbjct: 3   RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALEN 61

Query: 398 LDGT 401
            D +
Sbjct: 62  CDKS 65

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 18/52 (34%), Positives = 30/52 (57%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           R+FV  LS +VTE DL + F ++G +++V +   K+    +GFA +     E
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE 52

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVIL-PID----KETDKTKGFALVTFLMPEH 390
           S R++V+NLS  VTE+DL  +F ++   +       D     E  + KG A VTF   E 
Sbjct: 1   SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTE-GRMKGQAFVTFPSEEI 59

Query: 391 ATQAYQHLDGTVFLGR 406
           AT+A   ++G V  G+
Sbjct: 60  ATKALNLVNGYVLKGK 75

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 6/65 (9%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I V+NL       +L +LF K+G L  V+LP    T      A+V FL P  A  A++ L
Sbjct: 3   ILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGIT------AIVEFLEPSEAKLAFRKL 56

Query: 399 DGTVF 403
             + F
Sbjct: 57  AYSKF 61

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          + +  E LKA+FE+ GTV   ++    E G+ R F ++ +   + A+ A++  +   +  
Sbjct: 9  WSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDG 68

Query: 86 SRIKVEK 92
            I V+ 
Sbjct: 69 RPINVDF 75

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           D TL++ NL+   TE+ +   F + GP+  V + +  + K         + FV F    S
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPK------SFAFVTFKHEVS 54

Query: 640 LNQALKVLQNSSLDEHQIELK 660
           +  A+++L    L   ++ +K
Sbjct: 55  VPYAIQLLNGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  + T++ +R  F+  GPI S  + R +     GQ  S+GYGFV +      
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDR---ITGQ--SLGYGFVDYVDENDA 55

Query: 641 NQALKVLQNSSLDEHQIELKR 661
            +A+       L+  +I  KR
Sbjct: 56  QKAINT-----LNGFEIRNKR 71

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 8/70 (11%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNEAKRA 744
           K+ V N+P+     E++E F  FG++K   +P  K+   +GL +G+GFV F +++     
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKE---TGLSKGYGFVSFSSRDG---L 54

Query: 745 MKALCQSTHL 754
             AL +  H+
Sbjct: 55  ENALQKQKHI 64

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 24/66 (36%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            L+I NL+   TE  + + F K G I        K     GQ    GY FV F T+E   
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQ--PRGYCFVTFETKEEAE 58

Query: 642 QALKVL 647
           +ALK L
Sbjct: 59  KALKSL 64

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           ++ + N+  +  +  + +LF  +G++K       K     G  RG+ FV F TK EA++A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 745 MKALCQSTHLYGRRLVLEWA 764
           +K+L   T   G++LV+ WA
Sbjct: 61  LKSLNGKT-ALGKKLVVRWA 79

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 7/61 (11%)

Query: 704 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW 763
           +LF  FG ++ ++L KK        GF FVEF T+  A++A++ L       GR L +++
Sbjct: 3   KLFSPFGNVEKIKLLKK------KPGFAFVEFSTEEAAEKAVQYL-NGVLFGGRPLRVDY 55

Query: 764 A 764
           +
Sbjct: 56  S 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 43.3 bits (103), Expect = 2e-05
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 339 IFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +++ NL+  + +D+L +    LF ++GP+ +++     +T K +G A V F   E AT A
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATNA 58

Query: 395 YQHLDGTVFLGRMLHL 410
            + L G  F  + + +
Sbjct: 59  LRALQGFPFYDKPMRI 74

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 11/80 (13%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           +TT+++  L+   TED +R  F   G I  V     K P  PG+    G GFVQF  R +
Sbjct: 1   NTTVFVGGLDPAVTEDELRSLFGPFGEIVYV-----KIP--PGK----GCGFVQFVHRAA 49

Query: 640 LNQALKVLQNSSLDEHQIEL 659
              A++ LQ + +   +I L
Sbjct: 50  AEAAIQQLQGTIIGGSRIRL 69

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 14/94 (14%)

Query: 579 PDTTLYIKNLNFNSTED----SIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           P   +++ +L  + ++D    ++  HF K G +  V V R         +    Y FVQF
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLR--------DWRQRPYAFVQF 52

Query: 635 YTRESLNQALKVLQNSSLDEHQI--ELKRSNRNL 666
              +    AL   Q + LD   I  E  + NR L
Sbjct: 53  TNDDDAKNALAKGQGTILDGRHIRCERAKVNRTL 86

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 43.3 bits (102), Expect = 2e-05
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RIFV  + +   E+DL K F +YG + EV +  D+    +KG+  VTF   E A +  Q 
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQE 62

Query: 398 LDGTVFLGRMLHLIP 412
            +   F  + L++  
Sbjct: 63  ANRLCFRDKKLNIGQ 77

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 42.9 bits (102), Expect = 2e-05
 Identities = 20/70 (28%), Positives = 38/70 (54%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +++ +L +   E +L K F ++G +  + L   K+T K+KG+A V F  PE A    + +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 399 DGTVFLGRML 408
           +  +   R+L
Sbjct: 62  NNYLLFERLL 71

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL   VTE+ + +LF + GP+ +V +P DK+  K K FA V F        A   L
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 399 DGTVFLGRMLHL 410
           +G    GR L++
Sbjct: 63  NGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           I++R +P    + ++     + G E K VRL ++   +G  RGF FVEF++  EA R M+
Sbjct: 5   IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRK-TTGASRGFAFVEFMSLEEATRWME 63

Query: 747 A 747
            
Sbjct: 64  L 64

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 21/61 (34%), Positives = 36/61 (59%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  +   + ED+L  LFEK GP+ ++ L +D  + + +G+A +TF   E A +A +  
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 399 D 399
           D
Sbjct: 64  D 64

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 8/78 (10%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPL--------AEVILPIDKETDKTKGFALVTFLMPEH 390
           +FV NL    TE DL + F   G +         ++ L  DK+T + KG A VT+  P  
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 391 ATQAYQHLDGTVFLGRML 408
           A+ A +  +   F+G  +
Sbjct: 61  ASAAIEWFNNKDFMGNTI 78

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 28/73 (38%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FV NL   +TED+  KLF KYG   EV +      +K KGF  +       A  A   
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56

Query: 398 LDGTVFLGRMLHL 410
           LD T   GR L +
Sbjct: 57  LDDTPMRGRQLRV 69

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            ++V  +P++  + ++++ F  FGEL  V++ KK   +G  +GFGFV F    + +  +K
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQV-KKDPKTGQSKGFGFVRF---ADYEDQVK 56

Query: 747 ALCQSTHLYGRRL 759
            L Q   + GR  
Sbjct: 57  VLSQRHMIDGRWC 69

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 27/78 (34%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 339 IFVRNLS-YTVTEDDLTKLFEKYGPLAEV-ILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           + V NL+   VT D L  LF  YG +  V IL   K+T      AL+    P+ A  A  
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDT------ALIQMADPQQAQTALT 55

Query: 397 HLDGTVFLGRMLHLIPGK 414
           HL+G    G+ L +   K
Sbjct: 56  HLNGIRLHGKKLRVTLSK 73

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 8/67 (11%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 502
           + ++NL Y     DL+ LF  +G L  V +P       P G    V ++    A  AF  
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGF-AFVTYMIPEHAVKAFAE 63

Query: 503 LAYTKFK 509
           L  T F+
Sbjct: 64  LDGTVFQ 70

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 20/66 (30%), Positives = 40/66 (60%), Gaps = 2/66 (3%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S+I+V+N+P    +  + E F++ GE+  V++ +     G  R FGFV F ++ +A++A+
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRT--RDGKSRRFGFVGFKSEEDAQQAV 58

Query: 746 KALCQS 751
           K   ++
Sbjct: 59  KYFNKT 64

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            +T+E L+  F   G V  V+L    + + R FAF+ +   + A+AAL   N   +   
Sbjct: 8  PSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNGLVLDGR 66

Query: 87 RIK 89
           ++
Sbjct: 67 TLR 69

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL++ NL+++  ++ ++  F+K G +    V   ++        S G+G+V F + E   
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGR-----SRGFGYVDFESPEDAK 55

Query: 642 QALKVLQNSSLDEHQIELKRS 662
           +A++ +    LD   I +  S
Sbjct: 56  KAIEAMDGKELDGRPINVDFS 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 29 ITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          + ++ L A F   G + D+Q+   Y T+ K R FAF+ +   + A AA+D  N + +F  
Sbjct: 10 VDEKVLHAAFIPFGDIKDIQIPLDYETQ-KHRGFAFVEFEEPEDAAAAIDNMNESELFGR 68

Query: 87 RIKV 90
           I+V
Sbjct: 69 TIRV 72

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 15/64 (23%), Positives = 31/64 (48%)

Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
          ++T+E L   F + G +  V++     GK + FAF+ +  E     A+   N   +F   
Sbjct: 12 RVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRE 71

Query: 88 IKVE 91
          ++++
Sbjct: 72 LRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 9/75 (12%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRL---PKKMVGSGLHRGFGFVEFITKNEAKRA 744
           + V N+PF  ++ E+ + F+  G+++ VR+    K    +G+ +GFG+V F TK+    A
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRK----TGIGKGFGYVLFKTKDSVALA 57

Query: 745 MKALCQSTHLYGRRL 759
           +K       L GR++
Sbjct: 58  LKL--NGIKLKGRKI 70

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          +   Q+ L+  F+E G V DV++    +G+ + F  + +  E+ AQ AL+  +   +   
Sbjct: 9  WSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KSGEELLGR 67

Query: 87 RIKVE 91
           I+V+
Sbjct: 68 EIRVD 72

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 43.4 bits (102), Expect = 3e-05
 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
              + VRN+P+ A +  +   F  FG +++   P     +G  +G GFV F  +      
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYAL-PVIDKSTGRAKGTGFVCFKDQYTYNAC 59

Query: 745 MK 746
           +K
Sbjct: 60  LK 61

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 42.5 bits (101), Expect = 3e-05
 Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ V  +P  A + +V  LF+ +G ++ V + +    +G  +G  FV+F ++ EA++A++
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDK-DTGQSKGCAFVKFSSREEAQKAIE 59

Query: 747 ALCQSTHLYG 756
           AL     + G
Sbjct: 60  ALHGKVTMPG 69

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++FV NL    T ++L  LFEKYG    V      E D  K +  V     E A  A + 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGT---VT-----ECDVVKNYGFVHMEEEEDAEDAIKA 52

Query: 398 LDGTVFLGRMLH 409
           L+G  F+G+ ++
Sbjct: 53  LNGYEFMGKRIN 64

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 27/68 (39%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL   V E+ L +LF + GPL +V +  DKE  K K F  V F   E    A   L
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62

Query: 399 DGTVFLGR 406
           +G    GR
Sbjct: 63  NGIRLYGR 70

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 42.8 bits (100), Expect = 3e-05
 Identities = 21/70 (30%), Positives = 36/70 (51%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV +LS  +T +D+   F  +G +++  +  D  T K+KG+  V+F     A  A  H+
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 399 DGTVFLGRML 408
            G    GR +
Sbjct: 64  GGQWLGGRQI 73

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 11/81 (13%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV-ARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T+Y      +     ++R F+ CGP+  VT+ +R   P          + F+ F   E+ 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQP----------HAFITFENLEAA 50

Query: 641 NQALKVLQNSSLDEHQIELKR 661
             A++ L  +S+D + I+++R
Sbjct: 51  QLAIETLNGASVDGNCIKVQR 71

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 23/56 (41%), Positives = 33/56 (58%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           IFV  +   + ED+L  LFEK GP+ ++ L +D  T   +G+A VTF   E A +A
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 59

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 5/54 (9%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
           ++FV  L+  +TE+DL + F ++G + +V +P        + FA VTF  PE A
Sbjct: 2   KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVA 50

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 689 LVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           LVR++P +  + + E+L K FG        + M   G  +   F  F  +  A +A+  L
Sbjct: 3   LVRHLPPELSEDDKEDLLKHFGASSV----RVMSRRGKLKNTAFATFDNEQAASQALSRL 58

Query: 749 CQSTHLYGRRLVLEWA 764
            Q   L G+RLV+E+A
Sbjct: 59  HQLKIL-GKRLVVEYA 73

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 502
           + V+NLPY     DL+ LF  FG+L  V V          G    V FL    A  A+  
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGF-AYVLFLDPEDAVKAYKE 63

Query: 503 LAYTKFK 509
           L    F+
Sbjct: 64  LDGKVFQ 70

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 5/65 (7%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 504
           + V NLP  T   DLK LF  FG +  + +             VEF  +  A+ A  +L 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 505 YTKFK 509
             +  
Sbjct: 61  GKELG 65

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQA 643
           ++ N+ +++TE+ +   F + GP+ S  +   +D   P      GYGF +F   E+   A
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKP-----KGYGFCEFEDIETAASA 56

Query: 644 LKVLQNSSL 652
           ++ L     
Sbjct: 57  IRNLNGYEF 65

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 17/63 (26%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + ++V  +P    Q E+  LF+A G ++  ++ +  + +G   G+GFV+++ +N+A++A+
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRI-TGQSLGYGFVDYVDENDAQKAI 59

Query: 746 KAL 748
             L
Sbjct: 60  NTL 62

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 42.0 bits (99), Expect = 4e-05
 Identities = 17/48 (35%), Positives = 29/48 (60%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +IFV  L   VTE++  + F ++G + +  L  D +T +++GF  VTF
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF 48

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 42.5 bits (100), Expect = 4e-05
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET--DKTKGFALVTFLMPEHATQAY 395
           ++FV  +  + +E DL +LFE+YG + ++ +  D+     ++KG   VTF   + A +A 
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62

Query: 396 QHLDGTVFLGRMLHLIPGKP 415
             L     L  M H I  KP
Sbjct: 63  NALHNMKTLPGMHHPIQMKP 82

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 42.4 bits (99), Expect = 4e-05
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T++S+R HF++ G +    V R  + K      S G+GFV + + E ++ 
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKR-----SRGFGFVTYSSVEEVDA 59

Query: 643 ALKVLQNSSLDEHQIELKRS 662
           A+   +   +D   +E KR+
Sbjct: 60  AMNA-RPHKVDGRVVEPKRA 78

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           V N P    QS++ +LF+ +GE+  +R P         R F +V+F +   A  A+  L
Sbjct: 5   VTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNK--TRRFCYVQFTSPESAAAAVALL 61

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 10/78 (12%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           ++ +  +P++A++ +VE  FK +G ++ +          L  GFGFVEF    +A  A+ 
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREIN---------LKNGFGFVEFEDPRDADDAVY 51

Query: 747 ALCQSTHLYGRRLVLEWA 764
            L     L G R+++E A
Sbjct: 52  EL-NGKELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L ++N+ F +T+  +R  F   G + SV + +K D    G     G+ FV+F T++  
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD----GS--HRGFAFVEFVTKQEA 54

Query: 641 NQALKVLQNSSL 652
             A++ L+++ L
Sbjct: 55  QNAMEALKSTHL 66

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 17/69 (24%), Positives = 33/69 (47%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V+NL  ++TE +L + F K+G     +  +  E  K++  A + +   E A +A  +
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 398 LDGTVFLGR 406
            + T     
Sbjct: 62  FNNTYINTS 70

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
            +T+Y+ NL F+ T + + + F K G +  VT+ + K+ +      S G  F+ F  RE 
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRK-----SKGVAFILFLDRED 55

Query: 640 LNQALKVLQNSSL 652
            ++ +K L N  L
Sbjct: 56  AHKCVKALNNKEL 68

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++IKNL+ +    ++   F   G I S  VA  ++  S       GYGFV F T E+  +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGS------KGYGFVHFETEEAAVR 58

Query: 643 ALKVLQNSSLDEHQI 657
           A++ +    L++ ++
Sbjct: 59  AIEKVNGMLLNDKKV 73

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 42.0 bits (98), Expect = 5e-05
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY++NL  ++TE++I+  F K  P     V + +D           Y FV F+ RE    
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-----------YAFVHFFNREDAVA 52

Query: 643 ALKVLQNSSLDEHQIEL 659
           A+ V+    +D   IE+
Sbjct: 53  AMSVMNGKCIDGASIEV 69

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 353 LTKLFEKYGPLAEVIL--PIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
           L K+F K+G    V +  P+D ET KTKG+A V F  PE A +A + L+G   
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVD-ETGKTKGYAFVEFATPEEAKEAVKALNGYKL 75

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++ V N+S + T  +L   FE+YGP+ E         D  K +A V     E A +A + 
Sbjct: 2   KLHVGNISSSCTNQELRAKFEEYGPVIEC--------DIVKDYAFVHMERAEDAVEAIRG 53

Query: 398 LDGTVFLGRMLHL 410
           LD T F G+ +H+
Sbjct: 54  LDNTEFQGKRMHV 66

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 11/67 (16%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP-----KKMVGSGLHRGFGFVEFITKNEA 741
           ++ +RN+ +   + ++E+LF  +G L  V LP     KK       +GF FV ++    A
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP------KGFAFVTYMIPEHA 57

Query: 742 KRAMKAL 748
            +A   L
Sbjct: 58  VKAFAEL 64

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 46.0 bits (109), Expect = 6e-05
 Identities = 23/95 (24%), Positives = 34/95 (35%), Gaps = 7/95 (7%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
              RI++ NL   + ED + +L E +G L    L  D  T  +KG+A   +  P     A
Sbjct: 294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVA 353

Query: 395 YQHLDGTVFLGRMLH-------LIPGKPKENEGNV 422
              L+G       LH               + G  
Sbjct: 354 IAALNGKDTGDNKLHVQRACVGANQATIDTSNGMA 388

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +F+ +L    T+ DL +LF  +G +    + +DK T ++K F  V++  PE A  A + +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 399 DG 400
           +G
Sbjct: 61  NG 62

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+F+     +VTEDDL + F  +G + ++ +  DK+T ++KG A V F     A +A + 
Sbjct: 5   RLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEE 63

Query: 398 LDGTV 402
           ++G  
Sbjct: 64  MNGKC 68

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RIFV  +    TE++L   F ++G + +V +  D+    +KG+  VTF   E A +    
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKI-LA 61

Query: 398 LDGTVFLGRMLHLIP 412
           +    F G+ L++ P
Sbjct: 62  MGNLNFRGKKLNIGP 76

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 8/81 (9%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK---FVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           + V N+P +    +  EL   FG ++    V        +G  +G+GFVE+ +K  A +A
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSES----TGESKGYGFVEYASKASALKA 57

Query: 745 MKALCQSTHLYGRRLVLEWAE 765
              L     + GR+L ++WA+
Sbjct: 58  KNQL-DGKQIGGRKLQVDWAD 77

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 41.6 bits (98), Expect = 7e-05
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 4/66 (6%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA----TQA 394
           +F+  LS+  T + L + F K+G + E ++  D  T +++GF  VTF  P        Q 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 395 YQHLDG 400
              LDG
Sbjct: 61  PHELDG 66

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 41.6 bits (97), Expect = 7e-05
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +IFV  LS     +D+ + FE++G + + +L  DK T++ +GF  VTF
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 42.2 bits (100), Expect = 7e-05
 Identities = 27/97 (27%), Positives = 54/97 (55%), Gaps = 16/97 (16%)

Query: 686 SKILVRNIPFQAKQSEVEELF-KAFG-----------ELKFVRLPKKMVGSGLHR--GFG 731
           +++ +RN+P    + +++ELF KA             ++K +R  K++  +G  +  G+G
Sbjct: 1   TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60

Query: 732 FVEFITKNEAKRAMKALCQSTHLYG--RRLVLEWAEE 766
           FVEF     A +A++AL  +  ++G  +R ++E+A E
Sbjct: 61  FVEFTNHEHALKALRALNNNPEIFGPDKRPIVEFAIE 97

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.5 bits (97), Expect = 7e-05
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL Y V    L ++F   G +    +  DK+  K++G   VTF  P  A QA    
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAISMF 61

Query: 399 DGTVFLGRMLHL 410
           +G +   R +H+
Sbjct: 62  NGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 41.4 bits (98), Expect = 8e-05
 Identities = 21/67 (31%), Positives = 34/67 (50%)

Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
           +V +L   VTE  L ++F   GP+  + +  D  T ++ G+A V F  P  A +A   L+
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 400 GTVFLGR 406
             V  G+
Sbjct: 63  FDVIKGK 69

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 45.7 bits (108), Expect = 8e-05
 Identities = 38/192 (19%), Positives = 73/192 (38%), Gaps = 23/192 (11%)

Query: 578 EPDTT-----LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS-MGYGF 631
           +   T     LY+  +     E+++   F           A      S         + F
Sbjct: 168 QQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAF 227

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN-------VAKQT 684
           ++F T E    A+  L +       ++++R +  +     T +    N       V K  
Sbjct: 228 LEFRTVEEATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLV 286

Query: 685 GS--------KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
            S        +I + N+P    + +++EL ++FG+LK   L K  + +GL +G+ F E+ 
Sbjct: 287 NSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKD-IATGLSKGYAFCEYK 345

Query: 737 TKNEAKRAMKAL 748
             +    A+ AL
Sbjct: 346 DPSVTDVAIAAL 357

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 41.3 bits (96), Expect = 8e-05
 Identities = 22/72 (30%), Positives = 34/72 (47%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
              +++R L    T+ DL KL + YG +      +DK T+K KG+  V F  P  A +A 
Sbjct: 1   KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 396 QHLDGTVFLGRM 407
             L  +    +M
Sbjct: 61  TALKASGVQAQM 72

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 41.4 bits (97), Expect = 8e-05
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ NL+   TED +++ F+  GP+ +V +   K+ K       + YGFV+++       
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNK------GVNYGFVEYHQSHDAEI 54

Query: 643 ALKVLQNSSLDEHQIEL 659
           AL+ L    ++ ++I +
Sbjct: 55  ALQTLNGRQIENNEIRV 71

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 41.2 bits (96), Expect = 8e-05
 Identities = 19/48 (39%), Positives = 31/48 (64%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +IFV  LS   T +D+ + FE++G + + +L  DK T++ +GF  VTF
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.0 bits (97), Expect = 9e-05
 Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RI V+NL   VTED L + FE  G + +V + +     K++ F  V F   E A QA ++
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 398 LDGT 401
            + T
Sbjct: 61  FNKT 64

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 9/72 (12%)

Query: 227 IVVKNLPAGVKKKDLKAYF-KPLP-------LASVRTTFLGMAYIGFKDEKNCNKALN-K 277
           ++VKNLPA + + +LK +F K          L +       +A+IG+K E+   KA +  
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 278 NKSFWKGKQLNI 289
           N ++    ++++
Sbjct: 63  NNTYINTSKISV 74

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL+++NL +++T++ +   F + GPI    V + K  K        G+G+V F   E   
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKK-----CRGFGYVTFALEEDAK 55

Query: 642 QALKVLQNSSLDEHQIELK 660
           +AL+  + +     +I ++
Sbjct: 56  RALEEKKKTKFGGRKIHVE 74

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
          Y + +++L+  F + G +TDV+L    +GK + +A++ +  E+  Q AL
Sbjct: 9  YSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL 57

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y+  + + STED IR +F  CG I  + +    D    G+F   G  F+ F T E+  +
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPD---TGRF--RGIAFITFKTEEAAKR 55

Query: 643 ALK 645
           AL 
Sbjct: 56  ALA 58

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I V+N  Y  T ++L  LFE +G L  V++P           A+V F  P+ A  A++ L
Sbjct: 3   ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTI------AIVEFANPQQARLAFKAL 56

Query: 399 DGTVFLGRMLHL 410
               F   +L+L
Sbjct: 57  AYRRFKDSILYL 68

This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 14/82 (17%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR------GFGFVEFITKNEA 741
           + V N+ F   + ++ ELF   G++K + +       GL R      GF FVE+ T+ +A
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIM-------GLDRFTKTPCGFCFVEYYTREDA 53

Query: 742 KRAMKALCQSTHLYGRRLVLEW 763
           + A+K L   T L  R + ++W
Sbjct: 54  ENAVKYL-NGTKLDDRIIRVDW 74

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           +FV  L+   T++DL  +F ++G +   EVI   DK+T  +  +A + F   E   +AY 
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIR--DKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 397 HLDGTVFLGRMLH 409
            +D  +   R +H
Sbjct: 64  KMDNVLIDDRRIH 76

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 13/77 (16%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY++NL  ++TE+ +R  F + G      V R K  K         Y FV F  R+   +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGE-----VERVKKIKD--------YAFVHFEERDDAVK 50

Query: 643 ALKVLQNSSLDEHQIEL 659
           A++ +    L+   IE+
Sbjct: 51  AMEEMNGKELEGSPIEV 67

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 11/80 (13%)

Query: 687 KIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           K+L VRN+P    + ++ ELF  +GE++ V+  K          + FV F  +++A +AM
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD---------YAFVHFEERDDAVKAM 52

Query: 746 KALCQSTHLYGRRLVLEWAE 765
           + +     L G  + +  A+
Sbjct: 53  EEM-NGKELEGSPIEVSLAK 71

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL++ +L     E  I   F +CG + SV + R K         S GYGFV+F T E+  
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTG-----KSAGYGFVEFATHEAAE 55

Query: 642 QALK 645
           QAL+
Sbjct: 56  QALQ 59

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 18/49 (36%), Positives = 24/49 (48%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           V  L +  TE DL   F  +G L  V +  D +T ++KGF  V F   E
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYE 52

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 36/70 (51%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV +LS  +T DD+   F  +G +++  +  D  T K+KG+  V+F     A  A Q +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 399 DGTVFLGRML 408
            G    GR +
Sbjct: 64  GGQWLGGRQI 73

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +TE+S+R ++++ G +    V R  DP S     S G+GFV F     ++ 
Sbjct: 5   LFIGGLSFETTEESLRNYYEQWGKLTDCVVMR--DPASK---RSRGFGFVTFSCMNEVDA 59

Query: 643 ALKVLQNSSLDEHQIELKRS 662
           A+   +  ++D   +E KR+
Sbjct: 60  AMAA-RPHTIDGRVVEPKRA 78

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + ++V  +P    Q E+  LF + GE++  +L +  V +G   G+GFV ++   +A+RA+
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVNAKDAERAI 60

Query: 746 KAL 748
             L
Sbjct: 61  NTL 63

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 7/80 (8%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++I  LN+ +T+DS+R +F + G +   TV R           S G+GF+ F   +S+N+
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMR-----DSATGRSRGFGFLTFKKPKSVNE 55

Query: 643 ALKVLQNSSLDEHQIELKRS 662
            +K  +   LD   I+ KR+
Sbjct: 56  VMK--KEHILDGKIIDPKRA 73

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY--- 395
           +F+  L++  T+D L + F ++G + +  +  D  T +++GF  +TF  P+   +     
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 396 QHLDGTV 402
             LDG +
Sbjct: 61  HILDGKI 67

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 339 IFVRNLSYTVTEDD----LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           IFV+    ++ EDD    LT+ F   G +  V +P D+ET  +KGFA + F   +   +A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 395 YQHLDGTVFLGRMLH 409
              LDG+   G  L 
Sbjct: 62  L-ELDGSDLGGGNLV 75

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240957 cd12513, RRM3_RBM12B, RNA recognition motif 3 in RNA-binding protein 12B (RBM12B) and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 8/80 (10%)

Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGM--------AYIGFKDEKNCNKALN 276
           + I ++NLP  V+K+D++A+F  L L   + TFL          A++ FK  ++   AL 
Sbjct: 1   YYIHLENLPFSVEKRDIRAFFGDLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDYCAALA 60

Query: 277 KNKSFWKGKQLNIYKYSKDN 296
            +K     +++ ++  S+++
Sbjct: 61  HHKRVLYNREVYVFPISRED 80

This subgroup corresponds to the RRM3 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. . Length = 81

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V N+    T+ DL  LF+ +G + E     D      +GFA V     E A  A   L
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56

Query: 399 DGTVFLGRMLHLIPGK 414
            G    GR L    GK
Sbjct: 57  QGFPVHGRPLRCGWGK 72

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 18/67 (26%), Positives = 34/67 (50%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L  T+T+ +L +LF +YG +    +  D+ T  ++G   + F     A +A + L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 399 DGTVFLG 405
           +G    G
Sbjct: 63  NGQKPEG 69

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G ++ V  IP    + E+  +F++ G +  +RL   M   G +RG+ FV +  K+EAKRA
Sbjct: 1   GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRL--MMDFDGKNRGYAFVMYTQKHEAKRA 58

Query: 745 MKAL 748
           ++ L
Sbjct: 59  VREL 62

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPID-KETDKTKGFALVTFLMPEHATQAYQ 396
           +I VRN+ +  T  +L +LF  +G L  V LP     T   +GF  V F+  + A +A++
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 397 HL-DGTVFLGRMLHL 410
            L   T   GR L L
Sbjct: 62  ALCHSTHLYGRRLVL 76

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 23/72 (31%), Positives = 35/72 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV NLS    E  L +LF  +G +  V +  D  T++ KG+  V+    + A  A   L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 399 DGTVFLGRMLHL 410
           +G     R+L +
Sbjct: 332 NGYTLGNRVLQV 343

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 39.8 bits (94), Expect = 2e-04
 Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI----TGLVEFLQKNQAKAAFNSLAY 505
           + V+NLP      DL+  F P+G +  V +            VEF     A+AA   L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 506 TKFK 509
               
Sbjct: 61  LVLD 64

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT----GLVEFLQKNQAKAAFNSL 503
           V NL YRT P DL+ +FE +G++G V +P   Y         V F  K  A+ A +++
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V  +  Q  +  + E+F  +G+++ +RL + +V +G  +G+ FVE+  + +A RA + 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIV-TGFSKGYAFVEYEHERDALRAYRD 64

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW 763
           F  FGE+   R+ K M  +G  +G+GFV F+ K +A+ A++++     L GR +   W
Sbjct: 20  FAPFGEISDARVVKDM-QTGKSKGYGFVSFVKKEDAENAIQSM-NGQWLGGRAIRTNW 75

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 8/63 (12%)

Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
           E+  LF  FGE+ +V++P    G    +G GFV+F+ +  A+ A++ L Q T + G R+ 
Sbjct: 17  ELRSLFGPFGEIVYVKIP---PG----KGCGFVQFVHRAAAEAAIQQL-QGTIIGGSRIR 68

Query: 761 LEW 763
           L W
Sbjct: 69  LSW 71

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 11/64 (17%)

Query: 30 TQEQLKAKFEEKGTVT--DVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
          T E+L+A FE+ GTVT  DV          + + F+    E+ A+ A+   N       R
Sbjct: 12 TSEELRALFEKYGTVTECDV---------VKNYGFVHMEEEEDAEDAIKALNGYEFMGKR 62

Query: 88 IKVE 91
          I VE
Sbjct: 63 INVE 66

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  + Y  TED++   F   G + E+ L    +T + +G A +TF   E A +A   L
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 399 DGTVFLGRML 408
           DG    GR L
Sbjct: 60  DGEDMGGRFL 69

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 19/71 (26%), Positives = 36/71 (50%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +   NL+  + E  L  + +KYG + EV +    +T+K  G A V F   + A +  + L
Sbjct: 5   VTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKL 64

Query: 399 DGTVFLGRMLH 409
           + T  +G+++ 
Sbjct: 65  NQTSVMGKIIK 75

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 10/60 (16%)

Query: 686 SKILVRNIP-FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           S++ V N+   +  + ++EE+F  +G         K++G  LH+G+GFV+F  + +A+ A
Sbjct: 1   SRVFVGNLNTDKVSKEDLEEIFSKYG---------KILGISLHKGYGFVQFDNEEDARAA 51

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 25/79 (31%), Positives = 48/79 (60%), Gaps = 8/79 (10%)

Query: 686 SKILV-RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           SK+LV  N+ + A +  ++E+F+   +   +R+P+    +G  +G+ FVEF +  +AK A
Sbjct: 1   SKVLVVNNLSYSASEDSLQEVFE---KATSIRIPQN---NGRPKGYAFVEFESAEDAKEA 54

Query: 745 MKALCQSTHLYGRRLVLEW 763
           + + C +T + GR + LE+
Sbjct: 55  LNS-CNNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 8/79 (10%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
            + ++ L F++TE+ IR  F         + +    D +        G  +V+F + E  
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGR------PTGEAYVEFASPEDA 54

Query: 641 NQALKVLQNSSLDEHQIEL 659
            +AL+   N+ +    IE+
Sbjct: 55  RRALRKH-NNKMGGRYIEV 72

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 26/72 (36%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  N T+D IR  F   G I S  + R K     GQ  S+GYGFV +   E  
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDK---VTGQ--SLGYGFVNYVDPEDA 56

Query: 641 NQALKVLQNSSL 652
            +A+  L    L
Sbjct: 57  EKAINTLNGLRL 68

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGP-LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
           + N+S TV E+ +   FEK GP + ++ L  D E       ALV F  P  A +A   L+
Sbjct: 5   LFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG------ALVEFESPSDAGKASLSLN 58

Query: 400 GTVFLGRMLHL 410
           G+ F G+ + +
Sbjct: 59  GSQFGGKTIKI 69

This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 327 VQFAEDIAESGR---IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
           V +A    ES +   ++V NL  T+T+D L  +F KYG + +  +  DK T   +G A V
Sbjct: 181 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFV 240

Query: 384 TFLMPEHATQAYQHLDGTV 402
            F   E A +A   L+  +
Sbjct: 241 RFNKREEAQEAISALNNVI 259

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + V  +P    Q E+E+LF  +G +   R+    V +G+ RG GF+ F  + EA+ A+
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQV-TGISRGVGFIRFDKRIEAEEAI 60

Query: 746 KAL 748
           K L
Sbjct: 61  KGL 63

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVIL--PIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           V N+S   TE+ +  LF   G + E+ L    D           V +  PE    A  HL
Sbjct: 4   VTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVA-LHL 62

Query: 399 DGTVFLGRMLHLIP 412
             TVF+ R L ++P
Sbjct: 63  TNTVFIDRALIVVP 76

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.2 bits (93), Expect = 2e-04
 Identities = 22/69 (31%), Positives = 34/69 (49%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +++R L    T+ DL KL + YG +      +DK T+K KG+  V F  P  A +A   L
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

Query: 399 DGTVFLGRM 407
             +    +M
Sbjct: 70  KASGVQAQM 78

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
            ++ V NL + V++DD+ +LF ++G L +  +  D+ + ++ G A V F     A +A +
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMK 59

Query: 397 HLDGTVFLGR 406
             +G    GR
Sbjct: 60  QYNGVPLDGR 69

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 27/75 (36%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAAFNSL 503
           ILVKNLP+     D++ LF  +G L  V VP        G    VEF    +A  A N+L
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGF-AFVEFSTAKEALNAMNAL 61

Query: 504 AYTKFKEVPLYLEWA 518
             T      L L++A
Sbjct: 62  KDTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRL-----PKKMVGSGLHRGFGFVEFITKNE 740
           + + V+N+ F      + + FK      F R+     PK+  G  L  GFGFV F TK +
Sbjct: 1   ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRP-GQTLSMGFGFVGFKTKEQ 59

Query: 741 AKRAMKALCQSTHLYGRRLVLEWA 764
           A+ A+KA+     L G  LV++++
Sbjct: 60  AQAALKAM-DGFVLDGHTLVVKFS 82

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 5/86 (5%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
           P+P+  L +  L+  +TE  +R  F K GPIA V++   +  +      S G+ FV F  
Sbjct: 6   PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-----SRGFAFVYFEN 60

Query: 637 RESLNQALKVLQNSSLDEHQIELKRS 662
            +   +A +      LD  +I +  S
Sbjct: 61  VDDAKEAKERANGMELDGRRIRVDFS 86

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 39.0 bits (92), Expect = 3e-04
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 10/66 (15%)

Query: 597 IRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ 656
           + + F   G +  + + +KK           G+ FV+F T E+  +A++ L         
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKP----------GFAFVEFSTEEAAEKAVQYLNGVLFGGRP 50

Query: 657 IELKRS 662
           + +  S
Sbjct: 51  LRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           KI +  +P    + +V+EL ++FG+LK   L K    +GL +G+ F E++  +   +A+ 
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKD-SATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 747 AL 748
            L
Sbjct: 61  GL 62

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V N+ F+  + E+   F   G ++ VR+      SG  +GF FV+F     A  A+K 
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRM-MTFEDSGKCKGFAFVDFEEIEFATNALK- 58

Query: 748 LCQSTHLYGRRLVLEWAE 765
                HL GR L +E+ E
Sbjct: 59  ---GKHLNGRALRVEYGE 73

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
           V  +  +  + ++ + F  FGE++ + +  +       +   FV F T+  A++A + L 
Sbjct: 6   VGGLGERVTEKDLRDHFYQFGEIRSITVVPR-------QQCAFVTFTTREAAEKAAERLF 58

Query: 750 QSTHLYGRRLVLEWAE 765
               + GRRL L+W  
Sbjct: 59  NKLIINGRRLKLKWGR 74

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 19/55 (34%), Positives = 30/55 (54%)

Query: 463 DLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW 517
           +L++LF PFG++  V +PP    G V+F+ +  A+AA   L  T      + L W
Sbjct: 17  ELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLSW 71

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           ++FV  LS   TE+ + + F  +G +  + LP+D +T++ +GF  VT+   E
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEE 52

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 22/69 (31%), Positives = 38/69 (55%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +++R L    T++DL KL + +G +      +DK+T+K KG+  V F  PE A +A + L
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 399 DGTVFLGRM 407
           +G     + 
Sbjct: 63  NGRGVQAQF 71

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKA-FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           ++ + NIP+  K  ++++LF+   GE+ +V L K     G  RG G VEF  K   ++A+
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD--EEGKSRGCGVVEFKDKESVQKAL 58

Query: 746 KALCQSTHLYGRRLVL 761
           + +     L GR+LV+
Sbjct: 59  ETM-NRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 343 NLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTV 402
            L  +VTE  LT+ F +YGP+  V++      D+ +G ALV F   E A  A   + G  
Sbjct: 14  GLDESVTEQYLTRHFSRYGPVVHVVI------DRQRGQALVFFDKVEAAQAAVNEMKGRK 67

Query: 403 FLGRML 408
             GR L
Sbjct: 68  LGGRKL 73

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I++ +L +   E +L K F ++G +  V +   K+T  +K +  + FL PE A  A + +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 399 DGTVFLGRML--HLIP 412
           +  + +G++L  H++P
Sbjct: 62  NNYLLMGKVLQVHVLP 77

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 8/64 (12%)

Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           +KIL ++N+P +  +  +E LF  F   K VRL  +       RG  FVEF T+ +A  A
Sbjct: 2   NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR-------RGIAFVEFETEEQATVA 54

Query: 745 MKAL 748
           ++AL
Sbjct: 55  LQAL 58

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV+NL Y +T D+L ++FE      ++ LP  K+   +KG A + F     A +A +  
Sbjct: 6   LFVKNLPYNITVDELKEVFED---AVDIRLPSGKD-GSSKGIAYIEFKTEAEAEKALEEK 61

Query: 399 DGTVFLGR 406
            G    GR
Sbjct: 62  QGAEVDGR 69

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 17/47 (36%), Positives = 28/47 (59%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +FV  LS+  T+ DL + F K+G + +  + ID  T +++GF  V F
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLF 47

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FV  +S +VT++ L +LF+    L    L  D  T K+KGFA VT+  P  A  A + 
Sbjct: 2   RLFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEK 60

Query: 398 LDG 400
           L+G
Sbjct: 61  LNG 63

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 227 IVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNK-N 278
           + V NLP    ++DL+  F     + SVR          G A++ F+  ++  KAL   N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 279 KSFWKGKQLNI 289
                G++L +
Sbjct: 61  GKELDGRKLKV 71

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNS 502
           R+I V+NLP++    DLK LF PFG +  V +P  P G       V+F  K  A+ A   
Sbjct: 1   RLI-VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 503 LAYTKFKEVPLYLEWA 518
           +   K K  P+ ++WA
Sbjct: 60  VNGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 7/63 (11%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            ++ V N+P    + E +ELF  +GE+  V L K+       +GFGF+   T+  A++A 
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-------KGFGFIRLDTRTNAEKAK 54

Query: 746 KAL 748
             L
Sbjct: 55  AEL 57

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            L++  L F+ T++ + + FKK G + SV +   +  K        G  +V++    S +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPK------GLAYVEYENESSAS 57

Query: 642 QALKVLQNSSLDEHQIELKRSN 663
           QA+  +  + + E  I +  SN
Sbjct: 58  QAVLKMDGTEIKEKTISVAISN 79

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y+ +++ + +ED I+  F+  G I S ++A        G+    GYGF+++   +S   
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAP---DPETGKHK--GYGFIEYENPQSAQD 57

Query: 643 ALK 645
           A+ 
Sbjct: 58  AIA 60

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           N+P+   + +++E F+    +  VRLP++    G  RGFG+ EF  ++   +A+
Sbjct: 8   NLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL 60

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 4/71 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            ++      +    D+ +LFE  GP+ +V +     +   +  A +TF   E A  A + 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56

Query: 398 LDGTVFLGRML 408
           L+G    G  +
Sbjct: 57  LNGASVDGNCI 67

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++F+  LS+  T++ L   FE++G L + ++  D  T +++GF  VT+   E    A
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.7 bits (92), Expect = 4e-04
 Identities = 15/48 (31%), Positives = 30/48 (62%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           ++F+  LS+  TE+ L   +E++G L + ++  D  + +++GF  VTF
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)

Query: 338 RIFVRNL-SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           R+FV NL +  V+++DL ++F KYG +  + L         KG+  V F   E A  A  
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

Query: 397 HLDGTVFLG 405
             +G    G
Sbjct: 54  GENGREIAG 62

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 39.8 bits (94), Expect = 4e-04
 Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVI--------LPIDKETDKTKGFALVTFLMPEH 390
           ++V  L   +T ++  ++F K G + E          L  D+     KG AL  +L  E 
Sbjct: 4   VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENG-NLKGDALCCYLKEES 62

Query: 391 ATQAYQHLDGTVFLG 405
              A Q LDGT    
Sbjct: 63  VELAIQLLDGTEIGR 77

This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 92

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 26/70 (37%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-IDKETDKTKGFALVTFLMPEHATQAYQ 396
           +IFVRNL + +T     KL EK+     V+   I  E  K+KG   V F  PE A +A +
Sbjct: 1   QIFVRNLPFDLT---WQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACR 57

Query: 397 HLDGTVFLGR 406
            ++G    GR
Sbjct: 58  LMNGIKINGR 67

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V N+ Y  T ++L   F   G +  V +  DK +   KGFA + F   E + +    L
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE-SVRTALAL 60

Query: 399 DGTVFLGRMLHLIP 412
           D ++F GR + ++P
Sbjct: 61  DESLFRGRQIKVMP 74

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 10/67 (14%)

Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR 757
           ++ ++E+LF+ FG L    + K          F FVEF    +A +A++AL   + + G 
Sbjct: 13  REEDIEKLFEPFGPLVRCDIRKT---------FAFVEFEDSEDATKALEAL-HGSRIDGS 62

Query: 758 RLVLEWA 764
            L +E+ 
Sbjct: 63  VLTVEFV 69

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 26/72 (36%), Positives = 35/72 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV NLS    E  L +LF  +G +  V +  D  T+K KGF  VT    + A  A   L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 399 DGTVFLGRMLHL 410
           +G     R+L +
Sbjct: 64  NGYRLGDRVLQV 75

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           +S ++FV NL + +TED+L + F+++G + EV +       +   F  V F  PE
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
           + V+NLP+ T   +L+ LFE FG++  V +P    T        V F+    A  A++ L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 504 AYTKFK 509
             + F+
Sbjct: 62  DGSIFQ 67

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 22/80 (27%), Positives = 46/80 (57%), Gaps = 4/80 (5%)

Query: 686 SKILVRNIPFQAKQSEVEELF-KAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           S+++V+N+P    ++E++E F K  GE+  V+L +     G  R   F+ + T+ EA++A
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE--DGKSRRIAFIGYKTEEEAQKA 58

Query: 745 MKALCQSTHLYGRRLVLEWA 764
                 +T++   ++ +E+A
Sbjct: 59  KDYF-NNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 5/76 (6%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            L + NL    T++  R      G +    +       S     S GYGFV++ ++ S  
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVY-----SESTGESKGYGFVEYASKASAL 55

Query: 642 QALKVLQNSSLDEHQI 657
           +A   L    +   ++
Sbjct: 56  KAKNQLDGKQIGGRKL 71

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           +T+E+L  +F   G + +V L          FAFI + RE  A  A++  N++ + +  
Sbjct: 14 DVTKEELNERFSRHGKILEVNLIKRANHT-NAFAFIKFEREQAAARAVESENHSMLKNKT 72

Query: 88 IKVEK 92
          + V+ 
Sbjct: 73 MHVQY 77

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 6/64 (9%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  L   VTED+L  LF  +G +  V +P        KG   V F+    A  A Q L
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEAAIQQL 57

Query: 399 DGTV 402
            GT+
Sbjct: 58  QGTI 61

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 8/68 (11%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+++  L Y   E D+ + F+ YG + E+ L          GF  V F  P  A  A   
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYE 52

Query: 398 LDGTVFLG 405
           L+G    G
Sbjct: 53  LNGKELCG 60

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 39.4 bits (92), Expect = 5e-04
 Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 8/81 (9%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM---VGSGLHRGFGFVEFITKNEAK 742
           + I+++NIPF  ++ ++ ++ +  G    + LP        +G+ RG  F  F +  EA+
Sbjct: 2   TAIVIKNIPFSLRKEQLLDIIEDLG----IPLPYAFNYHFDNGVFRGLAFANFRSPEEAQ 57

Query: 743 RAMKALCQSTHLYGRRLVLEW 763
             ++AL     + GRRL +E+
Sbjct: 58  TVVEAL-NGYEISGRRLRVEY 77

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP 388
           ++F+  LS+  + D L   F K+G + E ++  D  T +++GF  VTF  P
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 39.1 bits (91), Expect = 5e-04
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G ++ V  IP    + E+  LF+  G++   RL   M  SG +RG+ FV + TK EA+ A
Sbjct: 1   GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRL--MMEFSGENRGYAFVMYTTKEEAQLA 58

Query: 745 MKAL 748
           ++ L
Sbjct: 59  IRIL 62

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 39.2 bits (91), Expect = 5e-04
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + N+P    Q + EEL + FG L+  F+   +    +G  +G+GFVE++ K+ A RA   
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSET---TGHSKGYGFVEYMKKDSAARAKSD 60

Query: 748 LCQSTHLYGRRLVLEWAE 765
           L     L  R L + W +
Sbjct: 61  LL-GKQLGSRTLYVHWTD 77

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVIL 368
           + +RNL   VTE DL  L   +G +  V+L
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLL 31

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 12/66 (18%)

Query: 581 TTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           TTL ++N+         +  HF K G I ++ V    +P+S           VQF T E 
Sbjct: 2   TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQV--NYNPES---------ALVQFSTSEE 50

Query: 640 LNQALK 645
             +A +
Sbjct: 51  AKKAYR 56

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.0 bits (90), Expect = 5e-04
 Identities = 21/69 (30%), Positives = 33/69 (47%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +++R L    T+ DL KL + YG +      +DK T++ KG+  V F  P  A +A   L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 399 DGTVFLGRM 407
                  +M
Sbjct: 67  KANGVQAQM 75

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 39.1 bits (92), Expect = 6e-04
 Identities = 15/52 (28%), Positives = 27/52 (51%)

Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
          +  E+LK  F + G +T  ++    EGK + F F+ +   + AQ A++  N 
Sbjct: 13 MDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNG 64

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 10/76 (13%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ V N+P      E+  LF+ +G          +    + + +GFV    + +A+ A+K
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYG---------TVTECDVVKNYGFVHMEEEEDAEDAIK 51

Query: 747 ALCQSTHLYGRRLVLE 762
           AL       G+R+ +E
Sbjct: 52  AL-NGYEFMGKRINVE 66

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 38.9 bits (90), Expect = 6e-04
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRNL+ TVTE+ L K F ++G L  V         K K +A V F   + A +A   +
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEERDAAVRAMDEM 55

Query: 399 DGTVFLGRMLHLIPGKP 415
           +G    G  + ++  KP
Sbjct: 56  NGKEIEGEEIEIVLAKP 72

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 6/74 (8%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T LYI NL  +  E  +    K  G + S  + R  D K      S G GF +  +RE  
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILR--DSKG----QSRGVGFARMESREKC 54

Query: 641 NQALKVLQNSSLDE 654
              +       L  
Sbjct: 55  EDIISKFNGKYLKG 68

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 17/48 (35%), Positives = 29/48 (60%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +IFV  LS    E+ + + F  +G +  + LP+D +T+K +GF  +TF
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITF 48

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R++VR      +E  + ++F  YG + EV +           FA V F   E A +A   
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDS 52

Query: 398 LDGTVF 403
           + G V 
Sbjct: 53  VHGKVL 58

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           G + V NL   +++ +L  LF ++G + ++     + + K      V F     A  A  
Sbjct: 2   GTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALD 56

Query: 397 HLDGTVFLGRMLHL 410
            L+G  FLG  L +
Sbjct: 57  ALNGRPFLGGRLKV 70

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 38.9 bits (91), Expect = 7e-04
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 11/82 (13%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA---RKKDPKSPGQFLSMGYGFVQFYTR 637
           T+LY++N+   +  D +RR F K GPI  V +      + P+        G+ +VQF   
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPR--------GFAYVQFEDV 52

Query: 638 ESLNQALKVLQNSSLDEHQIEL 659
                AL  L  +     +IE+
Sbjct: 53  RDAEDALYYLDRTRFLGREIEI 74

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V N+ +      ++  F+ FG +   R+      +G  RGFG+V+F +  +AK+A++
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDR-ETGRSRGFGYVDFESPEDAKKAIE 59

Query: 747 ALCQSTHLYGRRLVLEWA 764
           A+     L GR + ++++
Sbjct: 60  AM-DGKELDGRPINVDFS 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 38.7 bits (91), Expect = 7e-04
 Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y+ NL+   TE+ +   F + GP+ +V + + +  ++       GYGFV+F + E  + 
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAH-----QGYGFVEFLSEEDADY 55

Query: 643 ALKVLQNSSL 652
           A+K++    L
Sbjct: 56  AIKIMNMIKL 65

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           I VRN+PF     ++++LF+  G +  +R   K    G  +GFG V F +  +A+RA
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNV--LRADVKTDNDGRSKGFGTVLFESPEDAQRA 55

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 10/70 (14%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y+ NL   +T+  +   F+K GP+ SV VAR   P  P      G+ FV+F        
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN--P--P------GFAFVEFEDPRDAED 51

Query: 643 ALKVLQNSSL 652
           A++ L    +
Sbjct: 52  AVRALDGRRI 61

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           D TL++ NL     E+ +   F + GP+  VT+ + K+ K         +GFV F   ES
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPK------SFGFVCFKHSES 54

Query: 640 LNQALKVL 647
           +  A+ +L
Sbjct: 55  VPYAIALL 62

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 38.9 bits (91), Expect = 7e-04
 Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 5/73 (6%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEV-ILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           +I + N+   V  +DL  L   YG +     +P   ET        VT+  PE A QA  
Sbjct: 2   KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVN----VTYESPEQAQQAVN 57

Query: 397 HLDGTVFLGRMLH 409
            L+G  + G  L 
Sbjct: 58  KLNGHEYEGSKLK 70

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G +I +  +P    + E+  L +  G++  +R+   M  +G +RG+ FV F  K EAK A
Sbjct: 1   GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRM--MMDFNGNNRGYAFVTFSNKQEAKNA 58

Query: 745 MKAL 748
           +K L
Sbjct: 59  IKQL 62

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 38.9 bits (90), Expect = 7e-04
 Identities = 26/72 (36%), Positives = 35/72 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV NLS    E  L +LF  +G +  V +  D  T+K KGF  VT    + A  A   L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 399 DGTVFLGRMLHL 410
           +G     R+L +
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 38.7 bits (91), Expect = 8e-04
 Identities = 23/79 (29%), Positives = 45/79 (56%), Gaps = 6/79 (7%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           I V  +  +A++ +V + F  FGE+K   + L ++   +G  +G+  +E+ TK EA+ A+
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRR---TGFVKGYALIEYETKKEAQAAI 65

Query: 746 KALCQSTHLYGRRLVLEWA 764
           + L     L G+ + ++WA
Sbjct: 66  EGL-NGKELLGQTISVDWA 83

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 8/65 (12%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ NL+   TED +   F + GPI S  + R+             Y FV++Y   S   
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--------YAFVEYYDHRSAAA 52

Query: 643 ALKVL 647
           AL+ +
Sbjct: 53  ALQTM 57

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLA-EVILPIDKETDKTKGFALVTFLMPEHATQ 393
            +  I +R L  +VTE+D+      +G    +V L   K T  ++GFA V F+  E AT+
Sbjct: 1   PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60

Query: 394 AYQHLDGTVFLGR 406
             +   G + L  
Sbjct: 61  WMELNQGKLQLQD 73

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 38.3 bits (89), Expect = 8e-04
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S  + V NLSY+ +ED L ++FEK        + I +   + KG+A V F   E A +A 
Sbjct: 1   SKVLVVNNLSYSASEDSLQEVFEK-----ATSIRIPQNNGRPKGYAFVEFESAEDAKEAL 55

Query: 396 QHLDGTVFLGRMLHL 410
              + T   GR + L
Sbjct: 56  NSCNNTEIEGRSIRL 70

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 38.7 bits (90), Expect = 8e-04
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
           V N+P      E EEL +A+G ++   L    V +G  +G+GFVE++ K+ A +A   L 
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEV-TGHSKGYGFVEYMKKDSASKARLELL 62

Query: 750 QSTHLYGRRLVLEWAE 765
               L    L  +W +
Sbjct: 63  GKQ-LGESTLFAQWMD 77

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 9/79 (11%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFALVTFLMPEH 390
           I++  L   VTED L +LF   G +          + +  DKET + KG A VT+  P  
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59

Query: 391 ATQAYQHLDGTVFLGRMLH 409
           A  A +  +G  F G  + 
Sbjct: 60  AQAAIEWFNGYEFRGNKIK 78

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL+I NL   +T   +R  F++ G I  + +  KK   +P       Y F+Q+    S+ 
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDI--KKQGGNP------AYAFIQYADIASVV 55

Query: 642 QALKVLQNSSLDEHQIEL 659
           +A++ +    L  ++++L
Sbjct: 56  KAMRKMDGEYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.6 bits (90), Expect = 9e-04
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 594 EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQN 649
           E  +R  F++ G +  + V R +   S     S G  FV FYTR++  +A   L N
Sbjct: 15  EKDLRELFEQYGAVYQINVLRDR---SQNPPQSKGCCFVTFYTRKAALEAQNALHN 67

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of calcineurin (RCANs) and similar proteins

 Score = 38.3 bits (90), Expect = 9e-04
 Identities = 27/80 (33%), Positives = 33/80 (41%), Gaps = 17/80 (21%)

Query: 339 IFVRNLSYTVTEDDLTK-----LFEKYGPLAE-VILPIDKETDKTKGF--ALVTFLMPEH 390
           + V N+   V  +   K     LF  YG +A  V LP          F  A V F  PE 
Sbjct: 1   LIVTNVPSEVFTNAELKAALESLFSSYGEIATFVYLP---------SFRRARVVFSSPEE 51

Query: 391 ATQAYQHLDGTVFLGRMLHL 410
           A  A   L GTVF G +L +
Sbjct: 52  AALARIELHGTVFEGSVLRV 71

This subfamily corresponds to the RRM of RCANs, a novel family of calcineurin regulators that are key factors contributing to Down syndrome in humans. They can stimulate and inhibit the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C) signaling in vivo through direct interactions with its catalytic subunit. Overexpressed RCANs may bind and inhibit calcineurin. In contrast, low levels of phosphorylated RCANs may stimulate the calcineurin signaling. RCANs are characterized by harboring a central short, unique serine-proline motif containing FLIISPPxSPP box, which is strongly conserved from yeast to human but is absent in bacteria. They consist of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. . Length = 75

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 8/63 (12%)

Query: 227 IVVKNLPAGVKKKDLKAYFKP---LPLASVRTT----FLGMAYIGFKDEKNCNKALNK-N 278
           ++VKNLP G+K+  L+  F+    +    ++ T    F    ++G+K E+   KAL   N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 279 KSF 281
            SF
Sbjct: 63  NSF 65

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 5/71 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++  L  N  +D ++  F   G +  V +   ++       L  GY +V+F + E   +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREV-----NLPRGYAYVEFESPEDAEK 55

Query: 643 ALKVLQNSSLD 653
           A+K +    +D
Sbjct: 56  AIKHMDGGQID 66

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 11/94 (11%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V  + +   +S++   F+ +G +K +RL +    +G  RG+ F+EF  + + K A K 
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKK-TGKPRGYAFIEFEHERDMKAAYKY 62

Query: 748 LCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
                 + GRR++++       VE  R RT + +
Sbjct: 63  -ADGKKIDGRRVLVD-------VE--RGRTVKGW 86

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 6/61 (9%)

Query: 701 EVEELFKAFGELKFVRL--PKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR 758
           ++ E+F  +G ++ V++   +K   +G  RGFGFV F +  +AK A +       + GRR
Sbjct: 15  DLREVFSRYGPIEKVQVVYDQK---TGRSRGFGFVYFESVEDAKEAKER-LNGMEIDGRR 70

Query: 759 L 759
           +
Sbjct: 71  I 71

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            ++ V +I F+  +  + + F  FG +K + +    V +  H+GF FVE+     A+ A+
Sbjct: 1   CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPV-TMKHKGFAFVEYEVPEAAQLAL 59

Query: 746 KALCQSTHLYGRRL 759
           + +     L GR +
Sbjct: 60  EQM-NGVMLGGRNI 72

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 17/66 (25%), Positives = 32/66 (48%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          Y +T+E L+  F   G V  V++ Y   G+    A + + + + A+ A+  FN   +   
Sbjct: 10 YDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQ 69

Query: 87 RIKVEK 92
           ++VE 
Sbjct: 70 PMQVEL 75

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 28 KITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
            T+E ++A FEE G + +V  ++    G+ +  AF+ +   ++AQ A++  +     
Sbjct: 10 TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTM 67

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE-SLN 641
           L++  L+ + TE  +   F + G ++ V + +KKD          G+ ++   T E  L 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPD-----RGFAYIDLRTSEAQLK 56

Query: 642 QALKVLQNS 650
           +    L  +
Sbjct: 57  KCKSTLNGT 65

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 5/66 (7%)

Query: 699 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR 758
           ++ V E F  +G L FV++ +        R + FV+F   ++AK A+ A  Q T L GR 
Sbjct: 20  EAAVTEHFSKYGTLVFVKVLRDWRQ----RPYAFVQFTNDDDAKNAL-AKGQGTILDGRH 74

Query: 759 LVLEWA 764
           +  E A
Sbjct: 75  IRCERA 80

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           D TL++ NL+   TE+ I   F + GP+  V + + KD K P QF      FV F    S
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGK-PKQF-----AFVNFKHEVS 54

Query: 640 LNQALKVLQNSSLDEHQIELK 660
           +  A+ +L    L    + ++
Sbjct: 55  VPYAMNLLNGIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 9/79 (11%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L +  L + +TE  ++ +F   G +  V V  KKDPK+ GQ  S G+GFV+F   E    
Sbjct: 2   LIVLGLPWKTTEQDLKDYFSTFGELLMVQV--KKDPKT-GQ--SKGFGFVRFADYED--- 53

Query: 643 ALKVLQNS-SLDEHQIELK 660
            +KVL     +D    ++K
Sbjct: 54  QVKVLSQRHMIDGRWCDVK 72

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G++I V  IP    + E+  LF+  G +  +RL    + +GL+RG+ FV F TK  A+ A
Sbjct: 1   GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPL-TGLNRGYAFVTFCTKEAAQEA 59

Query: 745 MKALCQS 751
           +K L  +
Sbjct: 60  VK-LYNN 65

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 12/50 (24%), Positives = 23/50 (46%)

Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN 79
           Q  ++  FE+ G +  ++       K RRF ++ +   + A AA+   N
Sbjct: 13 DQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLN 62

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V N   +  + D+  LFE+YG +  +  P     +KT+ F  V F  PE A  A   L
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFP-SLRFNKTRRFCYVQFTSPESAAAAVALL 61

Query: 399 DGT 401
           +G 
Sbjct: 62  NGK 64

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           ++I V  IP    + E+ + F  FG +K V++      +G+ +G+GFV F T+ +A++ +
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR--AGVSKGYGFVTFETQEDAEKIL 60

Query: 746 K 746
            
Sbjct: 61  A 61

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 10/79 (12%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           +   N  + A+QSE+E LF  +G +  V          +  GF FV    + +A+ A++ 
Sbjct: 3   VFCGNFEYDARQSEIERLFGKYGRVDRV---------DMKSGFAFVYMEDERDAEDAIRG 53

Query: 748 LCQSTHLY-GRRLVLEWAE 765
           L         RRL +EWA+
Sbjct: 54  LDNFEFGRQRRRLRVEWAK 72

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 38.5 bits (89), Expect = 0.001
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + V  +P    Q E+E+LF  +G +   R+    V +G+ RG GF+ F  + EA+ A+
Sbjct: 3   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-TGVSRGVGFIRFDKRIEAEEAI 61

Query: 746 KAL 748
           K L
Sbjct: 62  KGL 64

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 16/93 (17%)

Query: 572 DEEREPEPDT-----TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
           + E E + D       LY++NL   +TE+ I + F +  P     V + +D         
Sbjct: 220 EPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------- 270

Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIEL 659
             Y FV F  RE   +A+  L    L+  +IE+
Sbjct: 271 --YAFVHFEDREDAVKAMDELNGKELEGSEIEV 301

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 38.5 bits (89), Expect = 0.001
 Identities = 24/72 (33%), Positives = 35/72 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV NL+    E  L ++F  +G +  V +  D  T+K KGF  VT    + A  A   L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 399 DGTVFLGRMLHL 410
           +G     R+L +
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 38.2 bits (88), Expect = 0.001
 Identities = 22/70 (31%), Positives = 32/70 (45%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  LS T    DL  LF KYG +    +  +  +   + +  VT    E AT+   HL
Sbjct: 4   LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 399 DGTVFLGRML 408
             T   GRM+
Sbjct: 64  HRTELHGRMI 73

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end) protein family

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 687 KILVRNIPFQAKQSEVEE-LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            + V N+P +    ++E+ L+  F   KF  +  +++  G      +V F    +A+ A 
Sbjct: 3   TLCVSNLPSKLSDEDIEDVLYHEFK--KFGDVSVRVLHDGEDERVAYVNFRHPEDAREAK 60

Query: 746 KALCQSTHLYGRRLVLEW 763
            A      L+ R L +E 
Sbjct: 61  HA-KGRLVLFDRPLNVEP 77

This subfamily corresponds to the RRM1 domain in the Spen (split end) family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also known as one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong- to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ +  +  +  ++++  +F  FG+++  R+ +     GL RG  FV F T+  A+ A+K
Sbjct: 3   KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIK 60

Query: 747 ALCQSTHLYG 756
           A+ Q+  + G
Sbjct: 61  AMHQAQTMEG 70

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRNL+ TVTE+ L K F ++G L  V         K K +A + F   + A +A + +
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEEM 55

Query: 399 DGTVFLGRMLHLIPGKP 415
           +G    G  + ++  KP
Sbjct: 56  NGKELEGENIEIVFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 2/79 (2%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           I++R +P  A ++++    +  G + + VRL +    SG  RGF FVEF    +A R M+
Sbjct: 5   IMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNK-SSGQSRGFAFVEFNHLQDATRWME 63

Query: 747 ALCQSTHLYGRRLVLEWAE 765
           A   S  + G+++ + +++
Sbjct: 64  ANQHSLMILGQKVSMHYSD 82

This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 85

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 20/66 (30%), Positives = 36/66 (54%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           E   +F+ +L    T+ DL + F  +G +    + IDK+T+ +K F  V++  P+ A  A
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

Query: 395 YQHLDG 400
            Q ++G
Sbjct: 63  IQAMNG 68

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 11/77 (14%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY++NL  ++TE++I + F    P A   V + +D           Y FV F  RE    
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD-----------YAFVHFSNREDAVD 59

Query: 643 ALKVLQNSSLDEHQIEL 659
           A+  L    +D   IE+
Sbjct: 60  AMNALNGKVIDGSPIEV 76

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 38.2 bits (88), Expect = 0.001
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + V  +P    Q E+E+LF  +G +   R+    V +G+ RG GF+ F  + EA+ A+
Sbjct: 6   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-TGVSRGVGFIRFDKRIEAEEAI 64

Query: 746 KAL 748
           K L
Sbjct: 65  KGL 67

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           T+Y+ NL+  +T D +   F + G +  V +A         Q     Y FV+F  + S+ 
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD-----ETQPTR--YAFVEFAEQTSVI 58

Query: 642 QALKVLQNSSLDEHQIELKRSN 663
            ALK L  +      +++  SN
Sbjct: 59  NALK-LNGAMFGGRPLKVNHSN 79

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 10/76 (13%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           KI V N+     Q E+  LF+A+G +         +   + R F FV    +  A RA++
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAV---------LSCAVMRQFAFVHLRGEAAADRAIE 52

Query: 747 ALCQSTHLYGRRLVLE 762
            L     L+GR+LV+E
Sbjct: 53  EL-NGRELHGRKLVVE 67

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 16/62 (25%), Positives = 32/62 (51%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV +LS  VT+  L   F  +   ++  +  D ++ +++G+  V+F   + A  A   +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 399 DG 400
           +G
Sbjct: 62  NG 63

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++FV  L   V E DLT+ F ++GP+ +  +  DK+T K +GF  V F   + A +A
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTY 82
          +K+ ++ L+  F + G V  +++   +   +G+    FAF+ +     A+ AL   N T 
Sbjct: 10 FKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ-LNGTE 68

Query: 83 VFSSRIKVEK 92
          +   +I V  
Sbjct: 69 LGGRKISVSL 78

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + V N+P Q  + E+ ++F+A+G +    L +    +GL RG  FV +  + EA+ A+
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKS-TGLPRGVAFVRYDKREEAQAAI 59

Query: 746 KAL 748
            +L
Sbjct: 60  SSL 62

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           +++ V N+ +   + ++EELF   GE+K V++      SG   G   V F  + +A+RA+
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKI--NYDRSGRSEGTADVVFEKREDAERAI 58

Query: 746 KAL 748
           K  
Sbjct: 59  KQF 61

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 36.7 bits (86), Expect = 0.002
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 34 LKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE 91
          L   F   G V  ++L          FAF+ +  E+ A+ A+ Y N        ++V+
Sbjct: 1  LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++++NL F+ T   ++  F++CG +    V    D +      S G+G V F + E   +
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGR------SKGFGTVLFESPEDAQR 54

Query: 643 ALKVLQNSSLDEHQIELK 660
           A+++     L+  ++E++
Sbjct: 55  AIEMFNGYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 13/81 (16%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFV---RLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           K+ V N+  +A + E+E+ F+ +G L+ V   R P          GF FVEF    +A+ 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---------GFAFVEFEDPRDAED 51

Query: 744 AMKALCQSTHLYGRRLVLEWA 764
           A++AL     + G R+ +E +
Sbjct: 52  AVRAL-DGRRICGNRVRVELS 71

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 37.5 bits (88), Expect = 0.002
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVIL---PIDKETDKTKGFALVTFLMPEHATQ 393
           G IF++NL  ++    L   F  +G     IL       E   +KG+  V F   E A +
Sbjct: 3   GNIFIKNLDKSIDNKALYDTFSAFGN----ILSCKVATDENGGSKGYGFVHFETEEAAVR 58

Query: 394 AYQHLDGTVFLGR 406
           A + ++G +   +
Sbjct: 59  AIEKVNGMLLNDK 71

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL   VTED L ++F+  GP+  V +  DK  +K   +  V +     A  A Q L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 399 DG 400
           +G
Sbjct: 60  NG 61

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 10/79 (12%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            L + NL+++++EDS++  F+K   I        + P++ G+    GY FV+F + E   
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSI--------RIPQNNGR--PKGYAFVEFESAEDAK 52

Query: 642 QALKVLQNSSLDEHQIELK 660
           +AL    N+ ++   I L+
Sbjct: 53  EALNSCNNTEIEGRSIRLE 71

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 9/59 (15%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           VR  P    +S + E+F  +G +K V++            F FVEF +   A RA  ++
Sbjct: 4   VRPFPPDTSESAIREIFSPYGAVKEVKMIS---------NFAFVEFESLESAIRAKDSV 53

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 9/110 (8%)

Query: 314 NIKAKHWKSQEDSVQFAEDIAESGRI-FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK 372
           ++ A  W   E+ V   ED+    +I +VRNL  T TE+ + K F ++ P         +
Sbjct: 212 HVIAVDWAEPEEEVD--EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKV------E 263

Query: 373 ETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNV 422
              K + +A V F   E A +A   L+G    G  + +   KP + +  V
Sbjct: 264 RVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYV 313

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 17/48 (35%), Positives = 31/48 (64%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           +IFV  L+   TE+ + + F ++G +  + LP+D +T+K +GF  +TF
Sbjct: 6   KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITF 53

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 15/49 (30%), Positives = 31/49 (63%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL 386
           ++F+  LS+  T++ L + F ++G + E ++  D  T +++GF  VTF+
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 50

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY++NL   ++ED+I++ F +  P     V + +D           Y FV F +RE    
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-----------YAFVHFTSREDAVH 52

Query: 643 ALKVLQNSSLDEHQIEL 659
           A+  L  + L+   IE+
Sbjct: 53  AMNNLNGTELEGSCIEV 69

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPI--DKETDKTKGFALVTFLMPEHATQAYQ 396
           ++V NL++  T++DL     + G +    +     K   K+KGFA V F     A    +
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 397 HLDGTVFLGR 406
            L+G  F G+
Sbjct: 61  KLEGREFNGK 70

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 22/62 (35%), Positives = 30/62 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IF+ NL     E  L ++F  +G +  V +  D  T+K KGF  VT    E A  A   L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 399 DG 400
           +G
Sbjct: 64  NG 65

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 19/67 (28%), Positives = 36/67 (53%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++FV ++  T+TE ++  +FE++G + EV +  DK T   +G   V +   + A +A + 
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 398 LDGTVFL 404
           L     L
Sbjct: 61  LHNQRTL 67

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 9/89 (10%)

Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
           ED++R       L+I NL+ N +E  +RR F K G I  V + R      P +     Y 
Sbjct: 2   EDDQRATR---NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKR------PARGQGGAYA 52

Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIEL 659
           F++F   +  ++A   +    +  + I++
Sbjct: 53  FLKFQNLDMAHRAKVAMSGRVIGRNPIKI 81

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++FV  LS+  ++ DL   F K+G + +  + +D  T +++GF  + F       +  + 
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 398 ----LDGTV 402
               LDG +
Sbjct: 61  KEHRLDGRL 69

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA----TQA 394
           +F+  LS+  T+ DL   F K+G + +  L +D  T +++GF  V F   E       Q 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 395 YQHLDGTV 402
              L+G V
Sbjct: 61  EHKLNGKV 68

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 17/62 (27%), Positives = 30/62 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I+V   + ++TE+ L + F +   L  + LP D  + K   +  + F   + AT A  H+
Sbjct: 1   IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 399 DG 400
            G
Sbjct: 61  TG 62

This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 15/81 (18%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV--ARKKDPKSPGQFLSMGYGFVQFYTRE 638
           TTL+I +L+   TE+ ++  F++ G I S+ +   R             G  +V   TR+
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR-------------GCAYVCMETRQ 49

Query: 639 SLNQALKVLQNSSLDEHQIEL 659
             ++AL+ L+N  L   +I++
Sbjct: 50  DAHRALQKLRNVKLAGKKIKV 70

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 12/73 (16%)

Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
           ED++R    + TL++ NL+   TE  +RR F + G I  V      D K PG+  +  YG
Sbjct: 1   EDDQR---ANRTLFLGNLDITVTETDLRRAFDRFGVITEV------DIKRPGRGQTSTYG 51

Query: 631 FVQFYTRESLNQA 643
           F++F   E+L+ A
Sbjct: 52  FLKF---ENLDMA 61

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 8/73 (10%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT-RES 639
           T + +KNL F +T+  +R  F   G + SV V +K D  +       G+ FV+F T +E+
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA------RGFAFVEFSTAKEA 54

Query: 640 LNQALKVLQNSSL 652
           LN A+  L+++ L
Sbjct: 55  LN-AMNALKDTHL 66

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           + L +KNL  + TE  ++ HF K G  I  V + R +D K      S    F+ + T E 
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK------SRRIAFIGYKTEEE 54

Query: 640 LNQALKVLQNSSLDEHQIE 658
             +A     N+ ++  +I 
Sbjct: 55  AQKAKDYFNNTYINTSKIS 73

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 37.1 bits (86), Expect = 0.003
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ +  + F   +  +E++F  +G++  V + K    +   RGFGFV F   ++AK AM 
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-ETQRSRGFGFVTFENPDDAKDAMM 60

Query: 747 AL 748
           A+
Sbjct: 61  AM 62

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S + V N+PF    +++ ++F  +G++  V + K    +   +G  F+ F+ + +A + +
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKE-TRKSKGVAFILFLDREDAHKCV 60

Query: 746 KALCQSTHLYGRRL 759
           KAL     L+GR L
Sbjct: 61  KALNN-KELFGRTL 73

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 5/53 (9%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALD 76
          Y+ T + L+  FE+ G V DV +   +YT E   R FAF+ ++ +  A+ A+D
Sbjct: 8  YRTTPDDLRRVFEKYGEVGDVYIPRDRYTRES--RGFAFVRFYDKRDAEDAMD 58

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 704 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
           ELF   G L+ V++PK    +G  + F FV F  +     A++ L     L+GR L ++
Sbjct: 20  ELFLQAGPLEGVKIPKD--PNGKPKSFAFVTFKHEVSVPYAIQLL-NGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV N+   VTE  L +LFE YG     +  +  E   ++G   V F     A +A + L
Sbjct: 4   LFVINVPRDVTESTLRRLFEVYGD----VRGVQTER-ISEGIVTVHFYDIRDAKRAVREL 58

Query: 399 DGTVFLGRML 408
            G     + L
Sbjct: 59  CGRHMQQQAL 68

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V  IP+ + + E+   F   GE++ + L      +G  RG  F+ F T+  AKRA+  
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDL-MTFPDTGRFRGIAFITFKTEEAAKRALA- 58

Query: 748 LCQSTHLYGRRLVLE 762
                 + GR L +E
Sbjct: 59  -LDGEDMGGRFLKVE 72

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 37.2 bits (86), Expect = 0.003
 Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + V  +P    Q E+E+LF  +G +   R+ +  + +G+ RG GF+ F  + EA+ A+
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQL-TGVSRGVGFIRFDKRIEAEEAI 59

Query: 746 KAL 748
           K L
Sbjct: 60  KGL 62

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 19/61 (31%), Positives = 31/61 (50%)

Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  L   +T+D++  LF   G +    L  DK T ++ G+  V ++ PE A +A   L+G
Sbjct: 6   VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65

Query: 401 T 401
            
Sbjct: 66  L 66

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 13/88 (14%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASV---TVARKKDPKSP-----GQFLSMGYGFVQ 633
           T+++ NL   + +  +++ FK+ GPI SV   +V  K+           +        V 
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 634 FY----TRESLNQALKVLQNSSLDEHQI 657
            Y      ES  +ALK L  +  + H I
Sbjct: 62  AYVVFKEEESAEKALK-LNGTEFEGHHI 88

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            ++V NL   + E ++  LF KYGP+ ++ L   K   +  G+A + F     A  A + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 398 LDGTVFLGRML 408
            DG  F G+ L
Sbjct: 58  RDGYDFDGQRL 68

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 37.4 bits (87), Expect = 0.003
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V N++Y VT D L ++F K+G     +L I   T   +  AL+ F     A  A   
Sbjct: 5   RVIVENMTYPVTLDVLHQIFSKFG----TVLKIITFTKNNQFQALIQFADAVSAQAAKLS 60

Query: 398 LDG 400
           LDG
Sbjct: 61  LDG 63

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 96

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 14/47 (29%), Positives = 21/47 (44%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           I +  LS   T   +   F  +G + E  L +D  T ++ G   VTF
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTF 47

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           IFV NL + V    L ++F   G +    +  DK+  K++G   VTF  P  A QA    
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKD-GKSRGMGTVTFEQPIEAVQAISMF 61

Query: 399 DGTVFLGRMLHL 410
           +G     R +H+
Sbjct: 62  NGQFLFDRPMHV 73

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFALVTFLMPEH 390
           IFV+ L   VT + +   F++ G +          + L  D+ET K KG A V+F  P  
Sbjct: 5   IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64

Query: 391 ATQAYQHLDGTVFLGR 406
           A  A    DG  F G 
Sbjct: 65  AKAAIDWFDGKEFSGN 80

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           L+I+NL +  TE+ + + F K GP++ V +   K  K P      G+ FV +
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP-----KGFAFVTY 51

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 36.8 bits (86), Expect = 0.004
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          Y  T+ +L+ +FEE G +  ++L      GK R +AFI +  E   +AA  Y +   +  
Sbjct: 11 YDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDG 70

Query: 86 SRIKVE 91
           R+ V+
Sbjct: 71 RRVLVD 76

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++  L   +TE+ +R  F++ G I  VT+ R KD        S G  FV+F +RE   +
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQ-----SKGCAFVKFSSREEAQK 56

Query: 643 ALKVLQNS 650
           A++ L   
Sbjct: 57  AIEALHGK 64

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 10/77 (12%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL+++N+N N  ++ +R  F++ G I ++  A K            G+  V +Y   +  
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACK----------HRGFIMVSYYDIRAAR 52

Query: 642 QALKVLQNSSLDEHQIE 658
           +A + LQ + L   +++
Sbjct: 53  RAKRALQGTELGGRKLD 69

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 18/64 (28%), Positives = 30/64 (46%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          YK+  ++LK  F+  G V    +K   EGK R    + +    +A  A+  FN   +F  
Sbjct: 8  YKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDR 67

Query: 87 RIKV 90
           ++V
Sbjct: 68 PMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.8 bits (85), Expect = 0.004
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 338 RIFVRNLSYTVTE-DDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           ++ +RNL +++ +   L K+F +YG + E  +P  +   K  GFA VT    ++A  A +
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALE 60

Query: 397 HLDGTVFLGRML 408
           + +G    GR +
Sbjct: 61  NTNGLEIDGRPV 72

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 9/63 (14%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFG----ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           + +R +PF A + ++ + F         +  V         G   G  +VEF +  +A+R
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-----GRPTGEAYVEFASPEDARR 56

Query: 744 AMK 746
           A++
Sbjct: 57  ALR 59

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++VRNL    +ED + K F ++ P         +   K + +A V F   E A  A  +L
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCV------ERVKKIRDYAFVHFTSREDAVHAMNNL 57

Query: 399 DGTVFLGRMLHLIPGKP 415
           +GT   G  + +   KP
Sbjct: 58  NGTELEGSCIEVTLAKP 74

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTF------LGMAYIGFKDEKNCNKALNKN 278
            T+ ++  P  VK+K ++ +F PL   ++R          G A++  K E++  KAL +N
Sbjct: 1   FTVKMRGAPFNVKEKHIREFFSPLKPVAIRIVKNDHGRKTGFAFVDLKSEEDLKKALKRN 60

Query: 279 KSFWKGKQLNIY 290
           K +  G+ + ++
Sbjct: 61  KDYMGGRYIELF 72

This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEK-YGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           ++ V NL   VTE  + + F    GP+  V+L  + E  K+ G A +TF     AT+AY 
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYN-EGGKSTGIANITFKRAGDATKAYD 59

Query: 397 HLDGTVFLGR 406
             +G +  G 
Sbjct: 60  KFNGRIDDGN 69

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 29 ITQEQLKAKF-EEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF-SS 86
          +T+ Q++  F  + G +  V L Y   GK    A I + R   A  A D FN      + 
Sbjct: 11 VTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGNR 70

Query: 87 RIKVE 91
          ++KVE
Sbjct: 71 KMKVE 75

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 23/57 (40%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           RI+V NL   V E DL  LF KYG + ++ L   K       FA V F  P  A  A
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDA 54

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           GS++ +  IP    +  +  LF++ G L   RL   M  SGL+RGF + ++  +  A  A
Sbjct: 1   GSEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRL--MMTFSGLNRGFAYAKYSDRRGASAA 58

Query: 745 MKAL 748
           +  L
Sbjct: 59  IATL 62

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           G + + NL  TV+ + L  +F+ YG + E+     +ET   +    V F     A +A +
Sbjct: 2   GTLVIFNLDPTVSSETLRSIFQVYGDVKEL-----RETPCKREQRFVEFFDVRDAAKALR 56

Query: 397 HLDGTVFLGR 406
            ++G    G+
Sbjct: 57  AMNGKEISGK 66

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           I++R +P    ++++ EL ++F   +   VRL K+   +G+ RGF FVEF    +A   M
Sbjct: 8   IMLRGLPINITENDIRELIESFEGPQPADVRLMKRK--TGVSRGFAFVEFYHLQDATSWM 65

Query: 746 KALCQSTHLYGRRLVLEWA 764
           +A  +   + G+ + + ++
Sbjct: 66  EANQKKLVIQGKTIAMHYS 84

This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	787
KOG0110|consensus	725		100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0127|consensus	678		100.0
KOG0123|consensus	369		100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0127|consensus	678		100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0110|consensus	725		100.0
KOG0123|consensus	369		100.0
KOG0145|consensus	360		100.0
KOG0117|consensus	506		100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0145|consensus	360		100.0
KOG0117|consensus	506		100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.98
KOG0148|consensus	321		99.97
KOG0148|consensus	321		99.97
KOG4211|consensus	510		99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
KOG0144|consensus	510		99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.96
KOG0144|consensus	510		99.96
KOG1190|consensus	492		99.95
KOG1190|consensus	492		99.95
KOG4211|consensus	510		99.94
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.94
KOG4212|consensus	608		99.93
KOG0147|consensus	549		99.93
KOG0124|consensus	544		99.92
KOG1456|consensus	494		99.92
KOG0124|consensus	544		99.92
KOG0131|consensus	203		99.92
KOG0147|consensus	549		99.91
KOG4212|consensus	608		99.91
KOG4307|consensus	944		99.9
KOG1365|consensus	508		99.9
KOG0146|consensus	371		99.86
KOG0131|consensus	203		99.84
KOG1456|consensus	494		99.83
KOG0109|consensus	346		99.82
KOG0109|consensus	346		99.79
KOG0146|consensus	371		99.78
KOG4307|consensus	944		99.75
KOG1365|consensus	508		99.74
KOG0120|consensus	500		99.74
KOG4205|consensus	311		99.73
KOG0120|consensus	500		99.72
KOG0105|consensus	241		99.7
KOG0105|consensus	241		99.69
KOG4206|consensus	221		99.68
KOG4205|consensus	311		99.68
KOG4206|consensus	221		99.62
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.62
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.61
KOG1548|consensus	382		99.55
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.5
KOG0106|consensus	216		99.5
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.49
KOG4207|consensus	256		99.48
KOG0122|consensus	270		99.47
KOG1548|consensus	382		99.47
KOG1457|consensus	284		99.45
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.45
KOG0121|consensus	153		99.43
KOG1457|consensus	284		99.42
KOG0106|consensus	216		99.41
KOG0125|consensus	376		99.4
KOG0122|consensus	270		99.4
PLN03120	260	nucleic acid binding protein; Provisional	99.39
KOG0125|consensus	376		99.38
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.37
KOG0114|consensus	124		99.36
PLN03120	260	nucleic acid binding protein; Provisional	99.35
KOG4207|consensus	256		99.35
KOG0149|consensus	247		99.33
KOG0149|consensus	247		99.32
KOG0107|consensus	195		99.31
KOG0121|consensus	153		99.31
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.3
smart00360	71	RRM RNA recognition motif.	99.29
KOG0111|consensus	298		99.28
PLN03213	759	repressor of silencing 3; Provisional	99.28
PLN03213	759	repressor of silencing 3; Provisional	99.27
KOG0126|consensus	219		99.27
smart00362	72	RRM_2 RNA recognition motif.	99.26
KOG0114|consensus	124		99.25
KOG0130|consensus	170		99.24
KOG0130|consensus	170		99.24
PLN03121	243	nucleic acid binding protein; Provisional	99.23
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.22
smart00361	70	RRM_1 RNA recognition motif.	99.21
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.21
PLN03121	243	nucleic acid binding protein; Provisional	99.2
KOG0107|consensus	195		99.2
KOG0113|consensus	335		99.19
smart00362	72	RRM_2 RNA recognition motif.	99.17
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
KOG0126|consensus	219		99.15
KOG0108|consensus	435		99.15
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.14
KOG0128|consensus	881		99.13
smart00360	71	RRM RNA recognition motif.	99.13
KOG0113|consensus	335		99.12
KOG0111|consensus	298		99.11
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.1
KOG4660|consensus	549		99.07
KOG0108|consensus	435		99.03
smart00361	70	RRM_1 RNA recognition motif.	98.98
KOG0112|consensus	975		98.95
KOG4660|consensus	549		98.95
KOG4661|consensus	940		98.9
KOG0128|consensus	881		98.9
KOG0129|consensus	520		98.86
KOG0415|consensus	479		98.84
KOG4210|consensus	285		98.84
KOG0415|consensus	479		98.84
KOG0129|consensus	520		98.79
KOG4208|consensus	214		98.77
KOG0153|consensus	377		98.76
KOG4208|consensus	214		98.73
KOG0226|consensus	290		98.66
KOG0533|consensus	243		98.65
KOG0132|consensus	894		98.64
KOG0112|consensus	975		98.5
KOG0132|consensus	894		98.5
KOG4454|consensus	267		98.49
KOG4661|consensus	940		98.48
KOG4210|consensus	285		98.41
KOG0226|consensus	290		98.41
KOG0533|consensus	243		98.39
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.38
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.32
KOG0153|consensus	377		98.32
KOG4454|consensus	267		98.21
KOG0116|consensus	419		98.21
KOG0151|consensus	877		98.21
KOG0116|consensus	419		98.18
KOG4209|consensus	231		98.09
KOG4209|consensus	231		98.02
KOG4676|consensus	479		98.02
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.01
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.93
KOG4676|consensus	479		97.93
KOG0151|consensus	877		97.9
KOG2193|consensus	584		97.84
KOG2193|consensus	584		97.84
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.8
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.58
KOG0115|consensus	275		97.48
KOG1995|consensus	351		97.39
KOG2314|consensus	698		97.34
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.3
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.24
KOG1995|consensus	351		97.23
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.14
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.11
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.08
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.06
KOG0115|consensus	275		97.04
KOG2202|consensus	260		96.9
KOG3152|consensus	278		96.67
KOG2314|consensus	698		96.61
KOG1855|consensus	484		96.59
KOG2202|consensus	260		96.46
KOG3152|consensus	278		96.25
KOG1855|consensus	484		96.19
KOG4849|consensus	498		96.15
KOG1996|consensus	378		96.15
KOG1996|consensus	378		96.1
KOG2416|consensus	718		95.96
KOG4849|consensus	498		95.87
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.26
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.14
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.99
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.96
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.57
KOG2416|consensus	718		94.51
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.16
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.08
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	93.89
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.14
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.08
KOG0804|consensus	493		92.26
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.22
KOG2135|consensus	526		92.16
KOG4285|consensus	350		90.95
KOG4285|consensus	350		90.83
KOG2591|consensus	684		90.62
KOG2068|consensus	327		90.5
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	90.34
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.32
KOG2068|consensus	327		90.03
KOG2591|consensus	684		89.42
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	88.96
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	88.57
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	88.51
KOG2135|consensus	526		88.48
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	87.81
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	86.17
KOG0804|consensus	493		85.36
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	84.13
KOG4574|consensus	1007		84.1
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	83.39
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	82.91
KOG4574|consensus	1007		82.46
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	81.11
KOG2253|consensus	668		81.0

>KOG0110|consensus

Probab=100.00  E-value=1.3e-72  Score=595.71  Aligned_cols=616  Identities=44%  Similarity=0.740  Sum_probs=440.6

Q ss_pred             ecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCC
Q psy3345          51 YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPE  130 (787)
Q Consensus        51 ~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (787)
                      ++++|++|+||||+|.+.++|+.||++||++||++++|+|+.|++++++.+|++||++..+++..++....++....   
T Consensus         2 ~t~dGk~R~F~FiGf~~eeeA~~Ai~~fn~s~i~ts~i~Ve~~~~~gd~~kpr~wsk~a~~~~~~~k~~k~~~~~~~---   78 (725)
T KOG0110|consen    2 RTKDGKFRRFGFIGFKSEEEAQKAIKYFNKSFINTSRITVEFCKSFGDPNKPRPWSKYAKKSSEPKKKEKEEEEANI---   78 (725)
T ss_pred             cCCCCceeeeeEeeeccHHHHHHHHHHhhccccccceEEEEehhhcCCcccCcchhhhhhhhhhhhcccchhhhccc---
Confidence            57899999999999999999999999999999999999999999999999999999999998874444322211111   


Q ss_pred             CcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCCCc------------------cccccccccccccccCCCCcH
Q psy3345         131 HTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGEE------------------KEEENEDESNNQIAHADISDM  192 (787)
Q Consensus       131 ~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~  192 (787)
                      .++..++++....||+|++||.+|.+  ++ .+|.|+..+.                  +.+.... ....+....|+  
T Consensus        79 ~k~~~kk~k~~~~d~efqeFle~~~~--~~-~~w~n~~k~~~~~~~~~~~~d~~~~~~~~~~~~~~-~~~~~~~~~is--  152 (725)
T KOG0110|consen   79 KKEKEKKKKALKDDPEFQEFLEVHRR--QS-TSWENDGKSKEASKLLREDEDSAGKGESLEEEASK-EPKAAVGKNIS--  152 (725)
T ss_pred             cccccccccccccCHHHHHHHHHhcc--cc-hhhccccchhhhhhhhhhhhhccccccccchhhcc-CcchhccccHH--
Confidence            11123334457889999999999999  66 8999874311                  0000000 11122333444  


Q ss_pred             HHHhhc-cCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCCCCcceeecccceEEEeecChHhH
Q psy3345         193 EYLKLK-TKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNC  271 (787)
Q Consensus       193 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~~~g~afV~F~~~~~A  271 (787)
                      +|+.+. +...+....++.                    +++....+.|++..-..-|+.     --|+.++.|.+.+..
T Consensus       153 ey~~s~~~k~~~~a~~~d~--------------------~a~~~~~~~d~r~~~~~~~~~-----~~~~~k~~~~e~~~v  207 (725)
T KOG0110|consen  153 EYLKSKMVKAESEAEEEDS--------------------SAELVTQERDVRYAGKEQGVE-----AGGVIKIDFSEEEEV  207 (725)
T ss_pred             HHHHHHHhhhhhhcccccc--------------------cccccccccccccchhhcCcc-----ccceeeccCchHHhh
Confidence            777766 332221111100                    011111111221111111111     013445555554443


Q ss_pred             HHHHhcCCcccCCeeEEEeecccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHH
Q psy3345         272 NKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTED  351 (787)
Q Consensus       272 ~~Al~~~~~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~  351 (787)
                      ..+...+...+                                             ....++.++.+|||+||||.++++
T Consensus       208 ~~~~~~~~~~~---------------------------------------------~~~e~i~etgrlf~RNLpyt~~ee  242 (725)
T KOG0110|consen  208 KQASKANQESM---------------------------------------------GVEEDISETGRLFVRNLPYTSTEE  242 (725)
T ss_pred             hhccccccccc---------------------------------------------chhhHHHhhhhhhhccCCccccHH
Confidence            33322111110                                             012456677899999999999999


Q ss_pred             HHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCC-CCCCC-------
Q psy3345         352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN-EGNVD-------  423 (787)
Q Consensus       352 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-~~~~~-------  423 (787)
                      +|+.+|                       |||.|..++.|.+|...++|+.++||.|+|.+..++.. .....       
T Consensus       243 d~~~lf-----------------------a~v~~~~~~~avka~~~~D~k~fqgrmlhvlp~~~k~~~~~~~~~~~~~~k  299 (725)
T KOG0110|consen  243 DLLKLF-----------------------AFVTFMFPEHAVKAYSELDGKVFQGRMLHVLPSKEKSTAKEDASELGSDYK  299 (725)
T ss_pred             HHHHhh-----------------------HHHhhhhhHHHHhhhhhccccccccceeeecCcchhhhhhhhHhhcCCcHH
Confidence            999999                       89999999999999999999999999999998876521 10000       


Q ss_pred             ------------------------------------------------CC-ccccccc---------------cccchhh
Q psy3345         424 ------------------------------------------------GK-VHCCISE---------------RKLDAFN  439 (787)
Q Consensus       424 ------------------------------------------------~~-~~~a~~~---------------~~~~~~~  439 (787)
                                                                      ++ +++++++               +.++.|+
T Consensus       300 ~~ke~~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~~i~d~~~~gsavr~al~etr~~~e~~~~~ee~gV~l~~F~  379 (725)
T KOG0110|consen  300 KEKELKRKAASASFHSWNTLFMGANAVAGILAQKLGVEKSRILDGSLSGSAVRLALGETRVVQEVRRFFEENGVKLDAFS  379 (725)
T ss_pred             HHHHhccccchhcceecccccccccHHHHHHHHHhCCeeeeeechhhcchHHHHHHHHhhhchhhhhhHHhhCcccccch
Confidence                                                            22 2444444               3355555


Q ss_pred             hhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEec
Q psy3345         440 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  519 (787)
Q Consensus       440 ~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  519 (787)
                      .  ..+..+.|+|+|||..+..++|..+|..||.|.++.+|+.|..|+|+|.++.+|+.|+..|++..+...+++++|+|
T Consensus       380 ~--~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP  457 (725)
T KOG0110|consen  380 Q--AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAP  457 (725)
T ss_pred             h--hhhhcceeeeccCccccccHHHHHHhhcccccceeecCcccceeeeeecCccchHHHHHHhchhhhccCccccccCh
Confidence            4  66778999999999999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             CccccccccccccccccccccccccchhhhhcccccccccCCCcc--cccccccccccCCCCCCeEEecCCCCCCCHHHH
Q psy3345         520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE--VEENVEEDEEREPEPDTTLYIKNLNFNSTEDSI  597 (787)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L  597 (787)
                      ..+|...+.......++....    +..........+........  ........ .......+.|||+||++++|.++|
T Consensus       458 ~dvf~~~pka~~~~~e~~~~~----ee~~~Er~s~~d~~v~eD~d~te~ss~a~~-a~~~~~~t~lfvkNlnf~Tt~e~l  532 (725)
T KOG0110|consen  458 EDVFTEDPKADDLSAESRSKM----EENPSERVSAEDGQVEEDKDPTEESSLARV-AEDEETETKLFVKNLNFDTTLEDL  532 (725)
T ss_pred             hhhccCCcccccccccccccc----ccCcceecccccccccccCCccccccchhh-hhccccchhhhhhcCCcccchhHH
Confidence            999875522222111111110    00000000001100000000  00000000 111222234999999999999999


Q ss_pred             HHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhhhhhcc
Q psy3345         598 RRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKS  677 (787)
Q Consensus       598 ~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~  677 (787)
                      ..+|...|.|.++.|.+.+++.+  .-.|+|||||+|.+.++|+.|++.|+|+.|+||.|.|+++.....   ....  .
T Consensus       533 ~~~F~k~G~VlS~~I~kkkd~~~--k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~---~~~g--K  605 (725)
T KOG0110|consen  533 EDLFSKQGTVLSIEISKKKDPAN--KYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPA---STVG--K  605 (725)
T ss_pred             HHHHHhcCeEEEEEEeccccccc--cccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccc---cccc--c
Confidence            99999999999999998887543  568999999999999999999999999999999999999982222   1111  2


Q ss_pred             ccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         678 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       678 ~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      .......+++|+|+|||+.++-.+|+.+|..||.|.+|+||+.. +.+.+||||||.|.++++|.+|+.+|. ++||+||
T Consensus       606 ~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~-~k~a~rGF~Fv~f~t~~ea~nA~~al~-STHlyGR  683 (725)
T KOG0110|consen  606 KKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKI-GKGAHRGFGFVDFLTPREAKNAFDALG-STHLYGR  683 (725)
T ss_pred             ccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhh-cchhhccceeeeccCcHHHHHHHHhhc-ccceech
Confidence            22233447899999999999999999999999999999999984 678899999999999999999999997 8999999


Q ss_pred             eEEEEEccccccHHHHHHHHhhhccCC
Q psy3345         758 RLVLEWAEEADNVEDIRKRTNRYFGTA  784 (787)
Q Consensus       758 ~l~v~~A~~~~~~~~~~~~~~~~~~~~  784 (787)
                      +|+++||..+..++++|+|++..|.+.
T Consensus       684 rLVLEwA~~d~~~e~~r~r~Aak~~~~  710 (725)
T KOG0110|consen  684 RLVLEWAKSDNTMEALRERTAAKFHDQ  710 (725)
T ss_pred             hhheehhccchHHHHHHHHHHHHhhcc
Confidence            999999999999999999999998764

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=100.00  E-value=2.6e-51  Score=469.90  Aligned_cols=353  Identities=25%  Similarity=0.383  Sum_probs=303.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCC
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE  417 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  417 (787)
                      +|||+|||+++|+++|+++|++||.|.+|+|+++..+++++|||||+|.+.++|.+|+..+++..+.|+.|+|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999976431


Q ss_pred             CCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC-----CCcEEEEEeCC
Q psy3345         418 NEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQ  492 (787)
Q Consensus       418 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~-----~~~~a~V~F~~  492 (787)
                      .                       .......+|+|+|||.++++++|+++|+.||.|.+|.+..     ++++|||+|.+
T Consensus        82 ~-----------------------~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~  138 (562)
T TIGR01628        82 S-----------------------LRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEK  138 (562)
T ss_pred             c-----------------------ccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECC
Confidence            1                       1122356799999999999999999999999999888754     35799999999


Q ss_pred             HHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccc
Q psy3345         493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEED  572 (787)
Q Consensus       493 ~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  572 (787)
                      .++|.+|+..++|..+.|+.|.|.+.....-         +                                       
T Consensus       139 ~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~---------~---------------------------------------  170 (562)
T TIGR01628       139 EESAKAAIQKVNGMLLNDKEVYVGRFIKKHE---------R---------------------------------------  170 (562)
T ss_pred             HHHHHHHHHHhcccEecCceEEEeccccccc---------c---------------------------------------
Confidence            9999999999999999999999976533200         0                                       


Q ss_pred             cccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy3345         573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL  652 (787)
Q Consensus       573 ~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l  652 (787)
                      ........++|||+|||+++|+++|+++|+.||.|.++.+..+..      +.++|||||+|.+.++|.+|+..|||..+
T Consensus       171 ~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~------g~~~G~afV~F~~~e~A~~Av~~l~g~~i  244 (562)
T TIGR01628       171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS------GRSRGFAFVNFEKHEDAAKAVEEMNGKKI  244 (562)
T ss_pred             ccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCC------CCcccEEEEEECCHHHHHHHHHHhCCcEe
Confidence            000123357899999999999999999999999999999998754      67899999999999999999999999999


Q ss_pred             C----CeEEEEEecCccccchhhhh----hhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCC
Q psy3345         653 D----EHQIELKRSNRNLESEATTV----KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS  724 (787)
Q Consensus       653 ~----g~~l~v~~~~~~~~~~~~~~----~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~  724 (787)
                      .    |+.|.|.++...........    ............++|||+|||..+|+++|+++|+.||.|++++|+.+  .+
T Consensus       245 ~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d--~~  322 (562)
T TIGR01628       245 GLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD--EK  322 (562)
T ss_pred             cccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC--CC
Confidence            9    99999998866544211110    01111122346788999999999999999999999999999999998  58


Q ss_pred             CCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccccH
Q psy3345         725 GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNV  770 (787)
Q Consensus       725 g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~  770 (787)
                      |.++|||||+|.+.++|.+|+..|| +..+.|++|.|.||..++..
T Consensus       323 g~~~g~gfV~f~~~~~A~~A~~~~~-g~~~~gk~l~V~~a~~k~~~  367 (562)
T TIGR01628       323 GVSRGFGFVCFSNPEEANRAVTEMH-GRMLGGKPLYVALAQRKEQR  367 (562)
T ss_pred             CCcCCeEEEEeCCHHHHHHHHHHhc-CCeeCCceeEEEeccCcHHH
Confidence            9999999999999999999999997 79999999999999977653

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=100.00  E-value=8.4e-47  Score=420.60  Aligned_cols=399  Identities=19%  Similarity=0.235  Sum_probs=289.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHh--CCceeCCeEEEEee
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL--DGTVFLGRMLHLIP  412 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l--~~~~~~g~~l~v~~  412 (787)
                      ++++|||+|||+++|+++|+++|++||.|.+|.++.      ++|||||+|.+.++|.+|++.+  ++..+.|+.|.|.+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~------~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP------GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC------CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            357899999999999999999999999999999875      3479999999999999999864  77899999999999


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCC--cEEEEEe
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG--ITGLVEF  490 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--~~a~V~F  490 (787)
                      +..++.....+..            . ..........|+|.||++.+++++|+++|+.||.|.+|.+.++.  ++|||+|
T Consensus        75 s~~~~~~~~~~~~------------~-~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef  141 (481)
T TIGR01649        75 STSQEIKRDGNSD------------F-DSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEF  141 (481)
T ss_pred             cCCcccccCCCCc------------c-cCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEE
Confidence            8754211110000            0 00011234579999999999999999999999999999887644  4899999


Q ss_pred             CCHHHHHHHHHHhcCCeeCC--eeEEEEEecCccccccccccccccccccccccccchhhhhc---ccccc---------
Q psy3345         491 LQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKE---NTAEE---------  556 (787)
Q Consensus       491 ~~~~~A~~A~~~l~~~~~~g--~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~---------  556 (787)
                      .+.++|.+|+..|||..+.|  ++|.|+|+..............+........ .+.+.....   .....         
T Consensus       142 ~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (481)
T TIGR01649       142 ESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLP-GRRDPGLDQTHRQRQPALLGQHPSSY  220 (481)
T ss_pred             CCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCC-CCCCCCcCccccccccccccCCCccC
Confidence            99999999999999999974  5899999876543322222221111100000 000000000   00000         


Q ss_pred             ------------------cccC---CCcc--------ccc--ccccccccCCCCCCeEEecCCCC-CCCHHHHHHHHhhc
Q psy3345         557 ------------------DNQQ---GVPE--------VEE--NVEEDEEREPEPDTTLYIKNLNF-NSTEDSIRRHFKKC  604 (787)
Q Consensus       557 ------------------~~~~---~~~~--------~~~--~~~~~~~~~~~~~~~l~V~NLp~-~~t~~~L~~~F~~~  604 (787)
                                        ....   ..+.        ...  ....-......++++|||+|||+ .+|+++|+++|+.|
T Consensus       221 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~y  300 (481)
T TIGR01649       221 GHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVY  300 (481)
T ss_pred             CCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhc
Confidence                              0000   0000        000  00000011134678999999998 69999999999999


Q ss_pred             CCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhh------------
Q psy3345         605 GPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT------------  672 (787)
Q Consensus       605 G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~------------  672 (787)
                      |.|.+|+++++.          +|||||+|.+.++|..|+..|||..|.|+.|.|.++..........            
T Consensus       301 G~V~~vki~~~~----------~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d  370 (481)
T TIGR01649       301 GNVERVKFMKNK----------KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKD  370 (481)
T ss_pred             CCeEEEEEEeCC----------CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCccccc
Confidence            999999998743          4899999999999999999999999999999999986532100000            


Q ss_pred             -----hhhcccc------ccCCCCCEEEEecCCccCcHHHHHHHHHhcCC--eeEEEeccccCCCCCCceEEEEEecCHH
Q psy3345         673 -----VKRKSSN------VAKQTGSKILVRNIPFQAKQSEVEELFKAFGE--LKFVRLPKKMVGSGLHRGFGFVEFITKN  739 (787)
Q Consensus       673 -----~~~~~~~------~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~--I~~v~i~~~~~~~g~~~g~afV~F~~~~  739 (787)
                           ..+....      ....++.+|||+|||..+|+++|+++|+.||.  |..+++....  + ..+|+|||+|.+.+
T Consensus       371 ~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~--~-~~~~~gfVeF~~~e  447 (481)
T TIGR01649       371 YSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD--N-ERSKMGLLEWESVE  447 (481)
T ss_pred             ccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC--C-CcceeEEEEcCCHH
Confidence                 0000000      01236789999999999999999999999998  8888886552  3 35899999999999


Q ss_pred             HHHHHHHHhcCCeeecCce------EEEEEcccc
Q psy3345         740 EAKRAMKALCQSTHLYGRR------LVLEWAEEA  767 (787)
Q Consensus       740 ~A~~Al~~l~~~~~~~Gr~------l~v~~A~~~  767 (787)
                      +|.+||..|| +..+.|+.      |+|+||++.
T Consensus       448 ~A~~Al~~ln-~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       448 DAVEALIALN-HHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             HHHHHHHHhc-CCccCCCCCCccceEEEEeccCC
Confidence            9999999997 69999985      999999763

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=100.00  E-value=4.6e-46  Score=426.57  Aligned_cols=347  Identities=26%  Similarity=0.396  Sum_probs=285.8

Q ss_pred             eEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-------ccceEEEeecChHhHHHHHh-cCCcccCCeeEEEeecccCC
Q psy3345         226 TIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-------FLGMAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYSKDN  296 (787)
Q Consensus       226 ~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-------~~g~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~~~~  296 (787)
                      +|||+|||+++|+++|+++|+.+|.+ +|+++       ++|+|||+|.+.++|++|+. +++..+.|+.|.|.      
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~------   75 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIM------   75 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEee------
Confidence            69999999999999999999999987 78887       45899999999999999998 78888999999994      


Q ss_pred             ccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCC
Q psy3345         297 SAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK  376 (787)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~  376 (787)
                                             |....    .........+|||+|||.++++++|+++|+.||.|.+|.++.+. +|+
T Consensus        76 -----------------------~s~~~----~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~  127 (562)
T TIGR01628        76 -----------------------WSQRD----PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGK  127 (562)
T ss_pred             -----------------------ccccc----ccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCC
Confidence                                   21000    00111234579999999999999999999999999999998874 688


Q ss_pred             cceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCC
Q psy3345         377 TKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLP  456 (787)
Q Consensus       377 ~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp  456 (787)
                      ++|||||+|.+.++|.+|++.+||..+.|+.|.|.....+....                    .......++|+|+|||
T Consensus       128 skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~--------------------~~~~~~~~~l~V~nl~  187 (562)
T TIGR01628       128 SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE--------------------AAPLKKFTNLYVKNLD  187 (562)
T ss_pred             cccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccc--------------------cccccCCCeEEEeCCC
Confidence            99999999999999999999999999999999997765431110                    0122345789999999


Q ss_pred             CCCCHHHHHHhhccCCCeeEEEecC-----CCcEEEEEeCCHHHHHHHHHHhcCCeeC----CeeEEEEEecCccccccc
Q psy3345         457 YRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFK----EVPLYLEWAPEGVFAEAK  527 (787)
Q Consensus       457 ~~~t~~~l~~~F~~~G~v~~v~i~~-----~~~~a~V~F~~~~~A~~A~~~l~~~~~~----g~~l~v~~~~~~~~~~~~  527 (787)
                      .++++++|+++|+.||.|.++.+..     .+++|||+|.+.++|.+|++.|+|..+.    |+.+.|.++....-....
T Consensus       188 ~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~  267 (562)
T TIGR01628       188 PSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAE  267 (562)
T ss_pred             CcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHH
Confidence            9999999999999999999988865     3469999999999999999999999999    999999887544100000


Q ss_pred             cccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCe
Q psy3345         528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI  607 (787)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v  607 (787)
                      .              .        .....             ...........++|||+|||+++++++|+++|+.||.|
T Consensus       268 ~--------------~--------~~~~~-------------~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i  312 (562)
T TIGR01628       268 L--------------R--------RKFEE-------------LQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEI  312 (562)
T ss_pred             H--------------H--------hhHHh-------------hhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCe
Confidence            0              0        00000             00011123456789999999999999999999999999


Q ss_pred             EEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCcccc
Q psy3345         608 ASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE  667 (787)
Q Consensus       608 ~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~  667 (787)
                      .+++++.+.      ++.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.++..
T Consensus       313 ~~~~i~~d~------~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~  366 (562)
T TIGR01628       313 TSAKVMLDE------KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ  366 (562)
T ss_pred             EEEEEEECC------CCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHH
Confidence            999999975      378999999999999999999999999999999999999987644

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=100.00  E-value=6e-43  Score=389.71  Aligned_cols=391  Identities=19%  Similarity=0.234  Sum_probs=277.7

Q ss_pred             cceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-ccceEEEeecChHhHHHHHh---cCCcccCCeeEEEeecccCCcc
Q psy3345         224 YHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-FLGMAYIGFKDEKNCNKALN---KNKSFWKGKQLNIYKYSKDNSA  298 (787)
Q Consensus       224 ~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-~~g~afV~F~~~~~A~~Al~---~~~~~l~g~~i~v~~~~~~~~~  298 (787)
                      +++|+|+|||+++++++|+++|+.||.| .+.++ .+|+|||+|.+.++|..|+.   .++..++|+.|.|.........
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~   81 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIK   81 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccc
Confidence            5799999999999999999999999998 67777 78999999999999999998   3678899999999521111000


Q ss_pred             ccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcc
Q psy3345         299 KYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTK  378 (787)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~  378 (787)
                       ...                  .    ............+|+|+||++.+|+++|+++|+.||.|.+|.++++.    .+
T Consensus        82 -~~~------------------~----~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~----~~  134 (481)
T TIGR01649        82 -RDG------------------N----SDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN----NV  134 (481)
T ss_pred             -cCC------------------C----CcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC----Cc
Confidence             000                  0    00000011223479999999999999999999999999999987653    24


Q ss_pred             eEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEeeCCCCCC-----CCCC---CCC-c--------------ccc----
Q psy3345         379 GFALVTFLMPEHATQAYQHLDGTVFLG--RMLHLIPGKPKEN-----EGNV---DGK-V--------------HCC----  429 (787)
Q Consensus       379 g~afV~F~~~~~A~~a~~~l~~~~~~g--~~l~v~~~~~~~~-----~~~~---~~~-~--------------~~a----  429 (787)
                      |+|||+|.+.++|.+|++.|||..|.|  ..|+|.++.....     ....   ..+ .              +..    
T Consensus       135 ~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~  214 (481)
T TIGR01649       135 FQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLG  214 (481)
T ss_pred             eEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCcccccccccccc
Confidence            699999999999999999999999965  5888888765310     0000   000 0              000    


Q ss_pred             --------------------------cccc----ccc-----------hhh--hhhhcCCCCEEEEeCCCC-CCCHHHHH
Q psy3345         430 --------------------------ISER----KLD-----------AFN--QVVEARSKRIILVKNLPY-RTLPTDLK  465 (787)
Q Consensus       430 --------------------------~~~~----~~~-----------~~~--~~~~~~~~~~i~v~nlp~-~~t~~~l~  465 (787)
                                                ++..    ...           ...  ......+.++|+|+|||+ .+++++|+
T Consensus       215 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~  294 (481)
T TIGR01649       215 QHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLF  294 (481)
T ss_pred             CCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHH
Confidence                                      0000    000           000  001123568999999998 69999999


Q ss_pred             HhhccCCCeeEEEecCC-CcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCcccccccccccccccccccccccc
Q psy3345         466 ALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEE  544 (787)
Q Consensus       466 ~~F~~~G~v~~v~i~~~-~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  544 (787)
                      ++|+.||.|.+|.+..+ +++|||+|.+.++|..|+..|+|..+.|++|.|.++...........           ....
T Consensus       295 ~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~-----------~~~~  363 (481)
T TIGR01649       295 NLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREG-----------QLDD  363 (481)
T ss_pred             HHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCC-----------cCcC
Confidence            99999999999998775 58999999999999999999999999999999999855422111000           0000


Q ss_pred             chhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCC--eEEEEEeecCCCCCCC
Q psy3345         545 GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP--IASVTVARKKDPKSPG  622 (787)
Q Consensus       545 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~--v~~v~i~~~~~~~~~~  622 (787)
                      +..     ...+......................+..+|||+|||+++++++|+++|+.||.  |..+++.....     
T Consensus       364 ~~~-----~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~-----  433 (481)
T TIGR01649       364 GLT-----SYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDN-----  433 (481)
T ss_pred             CCc-----ccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCC-----
Confidence            000     000000000000000000000112346789999999999999999999999998  88888764332     


Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE------EEEEecCc
Q psy3345         623 QFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ------IELKRSNR  664 (787)
Q Consensus       623 ~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~------l~v~~~~~  664 (787)
                        ..+|+|||+|.+.++|.+|+..|||..|+|+.      |+|.++..
T Consensus       434 --~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       434 --ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             --CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccC
Confidence              35799999999999999999999999999985      99988764

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0127|consensus

Probab=100.00  E-value=2.4e-41  Score=346.15  Aligned_cols=419  Identities=23%  Similarity=0.434  Sum_probs=295.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      .+|||++||++++.++|.++|+.+|+|..+.++.++.++.++||+||.|+-.+|+++|+..+++..+.|+.|.|.++..+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            68999999999999999999999999999999999988899999999999999999999999999999999999999877


Q ss_pred             CCCCCCC----CCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCC-----cEEE
Q psy3345         417 ENEGNVD----GKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG-----ITGL  487 (787)
Q Consensus       417 ~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-----~~a~  487 (787)
                      ..+....    .+......+...   .......+...|+|+|||+.+...+|..+|+.||.|..|.||..+     ||||
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~---~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaF  162 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRP---TKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAF  162 (678)
T ss_pred             ccchhcccccchhhhcccccCCc---chhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEE
Confidence            4333111    111111111000   011122347899999999999999999999999999999999732     6999


Q ss_pred             EEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCc-ccccccccc------ccccccccc----c------ccccchhhhh
Q psy3345         488 VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG-VFAEAKEKS------KGKEKEKNE----E------EGEEGEEEKK  550 (787)
Q Consensus       488 V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~-~~~~~~~~~------~~~~~~~~~----~------~~~~~~~~~~  550 (787)
                      |+|....+|..|++.+|+..|.||+|.|.||-.. .|.......      ....+...+    .      +..+.+....
T Consensus       163 V~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~ede  242 (678)
T KOG0127|consen  163 VQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDE  242 (678)
T ss_pred             EEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhccccccccc
Confidence            9999999999999999999999999999999554 343322110      000000000    0      0000000000


Q ss_pred             cccc------------ccc---ccCC---C--cccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEE
Q psy3345         551 ENTA------------EED---NQQG---V--PEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV  610 (787)
Q Consensus       551 ~~~~------------~~~---~~~~---~--~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v  610 (787)
                      +.+.            ++.   .++.   .  ++....+..........+.+|||+||||++|+++|.++|++||.|..+
T Consensus       243 Ee~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya  322 (678)
T KOG0127|consen  243 EETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYA  322 (678)
T ss_pred             ccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeE
Confidence            0000            000   0000   0  000000000112334456899999999999999999999999999999


Q ss_pred             EEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHh-----CC-CccCCeEEEEEecCccccchhh-------------
Q psy3345         611 TVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL-----QN-SSLDEHQIELKRSNRNLESEAT-------------  671 (787)
Q Consensus       611 ~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~l-----ng-~~l~g~~l~v~~~~~~~~~~~~-------------  671 (787)
                      .|+.+++     ++.|+|.|||.|.+..+|+.||.+.     .| ..|+||.|.|.++-........             
T Consensus       323 ~iV~~k~-----T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkr  397 (678)
T KOG0127|consen  323 IIVKDKD-----TGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKR  397 (678)
T ss_pred             EEEeccC-----CCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCcc
Confidence            9999887     8999999999999999999999976     24 6789999999887532211000             


Q ss_pred             ----------------------------------hhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHh----c-CCe
Q psy3345         672 ----------------------------------TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKA----F-GEL  712 (787)
Q Consensus       672 ----------------------------------~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~----~-G~I  712 (787)
                                                        ..+....+.-....++|.|+|||..++...|..+...    | +.+
T Consensus       398 NLyLa~EG~I~~gt~aAeglS~~Dm~kRer~~~~k~k~lknpnlhlSrtRL~i~Nlpramn~KqL~~Ll~~Av~~~at~~  477 (678)
T KOG0127|consen  398 NLYLAREGLIRDGTPAAEGLSATDMAKRERIAERKRKKLKNPNLHLSRTRLVIRNLPRAMNPKQLNRLLRDAVTGFATKV  477 (678)
T ss_pred             ceeeeccCccccCChhhcccchhhHHHHHHHHHHHHHhhcCCceeeehhhhhhhcCccccCHHHHHHHHHHHHhhhhhhc
Confidence                                              0000111112236788999999999999998888753    2 223


Q ss_pred             e-EEEecccc--CCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         713 K-FVRLPKKM--VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       713 ~-~v~i~~~~--~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      . .+|.++..  -..+.+.||+||.|..++.|..|+..+ + ..   ++-+|+|+....
T Consensus       478 kk~~R~~~~le~~~k~~s~g~aF~~f~EhEhalkalk~~-G-~l---kq~~Vefev~~~  531 (678)
T KOG0127|consen  478 KKCIRQIKFLEEEKKNYSEGYAFVGFTEHEHALKALKVL-G-VL---KQAKVEFEVDGV  531 (678)
T ss_pred             chhhhhhhhHHhhhhcccccccccCccHHHHHHHhhhcc-c-cc---ccceEEEEeccc
Confidence            2 24544442  124778999999999999999999876 1 21   466777776554

>KOG0123|consensus

Probab=100.00  E-value=1.4e-41  Score=357.61  Aligned_cols=341  Identities=26%  Similarity=0.392  Sum_probs=296.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCC
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE  417 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  417 (787)
                      .|||+   +++|+..|.++|+++|+++++++++|. |  +.|||||.|.++.+|.+|+.++|...+.|++|+|+|+... 
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd-   75 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD-   75 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC-
Confidence            58999   899999999999999999999999997 5  9999999999999999999999999999999999998743 


Q ss_pred             CCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC----CCcEEEEEeCCH
Q psy3345         418 NEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQK  493 (787)
Q Consensus       418 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~----~~~~a~V~F~~~  493 (787)
                                                   ...|+|+||+.+++..+|.++|+.||.|.+|++..    .+++ ||+|.++
T Consensus        76 -----------------------------~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e  125 (369)
T KOG0123|consen   76 -----------------------------PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESE  125 (369)
T ss_pred             -----------------------------CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCH
Confidence                                         12299999999999999999999999999999865    4467 9999999


Q ss_pred             HHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCccccccccccc
Q psy3345         494 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE  573 (787)
Q Consensus       494 ~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  573 (787)
                      ++|.+|+..+||..+.|+.|+|...........+.                                            .
T Consensus       126 ~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~--------------------------------------------~  161 (369)
T KOG0123|consen  126 ESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPL--------------------------------------------G  161 (369)
T ss_pred             HHHHHHHHHhcCcccCCCeeEEeeccchhhhcccc--------------------------------------------c
Confidence            99999999999999999999999875541111000                                            0


Q ss_pred             ccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy3345         574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD  653 (787)
Q Consensus       574 ~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~  653 (787)
                      + ....-+.++++|++.+++++.|..+|..+|.|.++.++.+..      +.++|||||.|.++++|..|+..||+...+
T Consensus       162 ~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~------g~~~~~gfv~f~~~e~a~~av~~l~~~~~~  234 (369)
T KOG0123|consen  162 E-YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSI------GKSKGFGFVNFENPEDAKKAVETLNGKIFG  234 (369)
T ss_pred             c-hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCC------CCCCCccceeecChhHHHHHHHhccCCcCC
Confidence            1 223457899999999999999999999999999999998775      568999999999999999999999999999


Q ss_pred             CeEEEEEecCccccchhhhh----hhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCce
Q psy3345         654 EHQIELKRSNRNLESEATTV----KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG  729 (787)
Q Consensus       654 g~~l~v~~~~~~~~~~~~~~----~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g  729 (787)
                      +..+.|..+.++........    .............+|||+||+..++.+.|+++|+.||.|.+++|+.+  ..|+++|
T Consensus       235 ~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~--~~g~skG  312 (369)
T KOG0123|consen  235 DKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD--ENGKSKG  312 (369)
T ss_pred             ccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEec--cCCCccc
Confidence            99999998877444221111    12222333567889999999999999999999999999999999998  6999999


Q ss_pred             EEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccccc
Q psy3345         730 FGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       730 ~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~  769 (787)
                      ||||+|.+.++|.+|+..+| +..+.|+.|.|.++.....
T Consensus       313 ~gfV~fs~~eeA~~A~~~~n-~~~i~~k~l~vav~qr~~~  351 (369)
T KOG0123|consen  313 FGFVEFSSPEEAKKAMTEMN-GRLIGGKPLYVAVAQRKED  351 (369)
T ss_pred             eEEEEcCCHHHHHHHHHhhC-hhhhcCCchhhhHHhhhcc
Confidence            99999999999999999997 6999999999999984443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.8e-40  Score=359.60  Aligned_cols=268  Identities=23%  Similarity=0.401  Sum_probs=227.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP  415 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  415 (787)
                      ..+|||+|||+++|+++|+++|+.||+|.+|+|++++.+|+++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            56899999999999999999999999999999999998999999999999999999999999999999999999987542


Q ss_pred             CCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHH
Q psy3345         416 KENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQ  495 (787)
Q Consensus       416 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~  495 (787)
                      ..                                                                              
T Consensus        83 ~~------------------------------------------------------------------------------   84 (352)
T TIGR01661        83 SS------------------------------------------------------------------------------   84 (352)
T ss_pred             cc------------------------------------------------------------------------------
Confidence            10                                                                              


Q ss_pred             HHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCccccccccccccc
Q psy3345         496 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEER  575 (787)
Q Consensus       496 A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  575 (787)
                                                                                                      
T Consensus        85 --------------------------------------------------------------------------------   84 (352)
T TIGR01661        85 --------------------------------------------------------------------------------   84 (352)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC-
Q psy3345         576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDE-  654 (787)
Q Consensus       576 ~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g-  654 (787)
                      .....++|||+|||+.+++++|+.+|++||.|..++++.+..     ++.++|||||+|.+.++|..|+..|||..+.| 
T Consensus        85 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~-----~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~  159 (352)
T TIGR01661        85 DSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNV-----TGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGC  159 (352)
T ss_pred             cccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCC-----CCCcCcEEEEEECCHHHHHHHHHHhCCCccCCC
Confidence            000124699999999999999999999999999999998764     45789999999999999999999999999987 


Q ss_pred             -eEEEEEecCccccchhh------------hhhh----------------------------------------------
Q psy3345         655 -HQIELKRSNRNLESEAT------------TVKR----------------------------------------------  675 (787)
Q Consensus       655 -~~l~v~~~~~~~~~~~~------------~~~~----------------------------------------------  675 (787)
                       ++|.|.++.........            ....                                              
T Consensus       160 ~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (352)
T TIGR01661       160 TEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQH  239 (352)
T ss_pred             ceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccccccc
Confidence             57888887533210000            0000                                              


Q ss_pred             --------------------ccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEe
Q psy3345         676 --------------------KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF  735 (787)
Q Consensus       676 --------------------~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F  735 (787)
                                          .........+.+|||+|||+.+++++|+++|++||.|.+++|+++. .+|.++|||||+|
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~-~t~~skG~aFV~F  318 (352)
T TIGR01661       240 AAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDL-TTNQCKGYGFVSM  318 (352)
T ss_pred             ccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcC-CCCCccceEEEEE
Confidence                                0000002234579999999999999999999999999999999985 6899999999999


Q ss_pred             cCHHHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         736 ITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       736 ~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      .+.++|.+||..|| |..|+||+|+|+|+..+.
T Consensus       319 ~~~~~A~~Ai~~ln-G~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       319 TNYDEAAMAILSLN-GYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             CCHHHHHHHHHHhC-CCEECCeEEEEEEccCCC
Confidence            99999999999997 799999999999998654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0127|consensus

Probab=100.00  E-value=5.7e-39  Score=328.78  Aligned_cols=303  Identities=23%  Similarity=0.347  Sum_probs=220.7

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      .-++|++     ||+++|.++|.++||.+|+|..+.++.++ .+.+||||||+|+-.||+++|++..+++.|.||.|.|.
T Consensus         6 ~TlfV~~-----lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~   80 (678)
T KOG0127|consen    6 ATLFVSR-----LPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVD   80 (678)
T ss_pred             ceEEEec-----CCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccc
Confidence            5689999     99999999999999999999999999987 57899999999999999999999999999999999999


Q ss_pred             EccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCCCc
Q psy3345          92 KCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGEE  171 (787)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (787)
                      +|++       +.-++.......            +.                        +..+..+.           
T Consensus        81 ~A~~-------R~r~e~~~~~e~------------~~------------------------veK~~~q~-----------  106 (678)
T KOG0127|consen   81 PAKK-------RARSEEVEKGEN------------KA------------------------VEKPIEQK-----------  106 (678)
T ss_pred             cccc-------cccchhcccccc------------hh------------------------hhcccccC-----------
Confidence            9987       211110000000            00                        00000000           


Q ss_pred             cccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCCCCc
Q psy3345         172 KEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA  251 (787)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v  251 (787)
                                                              .+...  -.....-.|+|+|||+.|.+.||...|+.||.+
T Consensus       107 ----------------------------------------~~~k~--~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V  144 (678)
T KOG0127|consen  107 ----------------------------------------RPTKA--KVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKV  144 (678)
T ss_pred             ----------------------------------------Ccchh--hccCccceEEeecCCcccCcHHHHHHHhhcceE
Confidence                                                    00000  001124579999999999999999999999988


Q ss_pred             -ceeec------ccceEEEeecChHhHHHHHh-cCCcccCCeeEEEeecccCCccccCC-----------------C--c
Q psy3345         252 -SVRTT------FLGMAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYSKDNSAKYSG-----------------A--A  304 (787)
Q Consensus       252 -~i~i~------~~g~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~~~~~~~~~~-----------------~--~  304 (787)
                       .|.|+      -.|+|||.|....+|..|+. +|+..+.||+|-|....+++......                 .  .
T Consensus       145 ~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~  224 (678)
T KOG0127|consen  145 VEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADE  224 (678)
T ss_pred             EEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhccccc
Confidence             88888      12899999999999999999 89999999999986433333322110                 0  0


Q ss_pred             CCCC-------ch-hhhhhh-hccc------------ccccchhh---------------hhcccCCCCeEEEcCCCCCC
Q psy3345         305 DDNN-------NA-SMENIK-AKHW------------KSQEDSVQ---------------FAEDIAESGRIFVRNLSYTV  348 (787)
Q Consensus       305 ~~~~-------~~-~~~~~~-~~~~------------~~~~~~~~---------------~~~~~~~~~~l~V~nLp~~~  348 (787)
                      +...       .. +..... ....            ........               .........+|||+||||++
T Consensus       225 d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~  304 (678)
T KOG0127|consen  225 DDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDT  304 (678)
T ss_pred             ccccccchhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccc
Confidence            0000       00 000000 0000            00000000               01122344899999999999


Q ss_pred             CHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHh-----CC-ceeCCeEEEEeeCCCC
Q psy3345         349 TEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL-----DG-TVFLGRMLHLIPGKPK  416 (787)
Q Consensus       349 te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l-----~~-~~~~g~~l~v~~~~~~  416 (787)
                      |+++|.++|++||+|..+.++.++.||.++|.|||.|.+..+|+.||+..     .| ..+.||.|.|.++..+
T Consensus       305 tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  305 TEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTR  378 (678)
T ss_pred             cHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccch
Confidence            99999999999999999999999999999999999999999999999865     23 6789999999998865

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=8.6e-38  Score=338.72  Aligned_cols=279  Identities=22%  Similarity=0.320  Sum_probs=215.0

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ++++|+|.|     ||+.+||+||+++|+.||+|.+|+|++++ +|+++|||||.|.+.+||.+||..||+..|.|+.|.
T Consensus         2 ~~~~l~V~n-----Lp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~   76 (352)
T TIGR01661         2 SKTNLIVNY-----LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIK   76 (352)
T ss_pred             CCcEEEEeC-----CCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEE
Confidence            467899999     99999999999999999999999999987 799999999999999999999999999999999999


Q ss_pred             EEEccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCC
Q psy3345          90 VEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDG  169 (787)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (787)
                      |.++++..                                                                        
T Consensus        77 v~~a~~~~------------------------------------------------------------------------   84 (352)
T TIGR01661        77 VSYARPSS------------------------------------------------------------------------   84 (352)
T ss_pred             EEeecccc------------------------------------------------------------------------
Confidence            99987500                                                                        


Q ss_pred             CccccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCCC
Q psy3345         170 EEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLP  249 (787)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~g  249 (787)
                                                                        .......|+|+|||.++++++|+++|..+|
T Consensus        85 --------------------------------------------------~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G  114 (352)
T TIGR01661        85 --------------------------------------------------DSIKGANLYVSGLPKTMTQHELESIFSPFG  114 (352)
T ss_pred             --------------------------------------------------cccccceEEECCccccCCHHHHHHHHhccC
Confidence                                                              000124699999999999999999999999


Q ss_pred             Cc-ceeec-------ccceEEEeecChHhHHHHHh-cCCcccCC--eeEEEeecccCCccc----cC-------CCcCC-
Q psy3345         250 LA-SVRTT-------FLGMAYIGFKDEKNCNKALN-KNKSFWKG--KQLNIYKYSKDNSAK----YS-------GAADD-  306 (787)
Q Consensus       250 ~v-~i~i~-------~~g~afV~F~~~~~A~~Al~-~~~~~l~g--~~i~v~~~~~~~~~~----~~-------~~~~~-  306 (787)
                      .+ .++++       ++|+|||+|.+.++|+.|+. +++..+.|  .+|.|..........    ..       ..... 
T Consensus       115 ~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (352)
T TIGR01661       115 QIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRV  194 (352)
T ss_pred             CEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCC
Confidence            87 56665       46899999999999999998 88888877  456664211111000    00       00000 


Q ss_pred             ------------CCch----------h-hhhh--h------hcccccc---c---ch--------hhhhcccCCCCeEEE
Q psy3345         307 ------------NNNA----------S-MENI--K------AKHWKSQ---E---DS--------VQFAEDIAESGRIFV  341 (787)
Q Consensus       307 ------------~~~~----------~-~~~~--~------~~~~~~~---~---~~--------~~~~~~~~~~~~l~V  341 (787)
                                  ....          . ....  .      ...+...   .   ..        .........+.+|||
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV  274 (352)
T TIGR01661       195 PLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFV  274 (352)
T ss_pred             CccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEE
Confidence                        0000          0 0000  0      0000000   0   00        000001123457999


Q ss_pred             cCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         342 RNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       342 ~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      +|||+++++++|+++|++||.|.+++|+++..+|.++|||||+|.+.++|.+|+..|||..|.||.|+|.+...+
T Consensus       275 ~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       275 YNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             eCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            999999999999999999999999999999889999999999999999999999999999999999999998765

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=100.00  E-value=5.5e-37  Score=336.59  Aligned_cols=286  Identities=22%  Similarity=0.325  Sum_probs=234.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEeeC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFL-GRMLHLIPG  413 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~-g~~l~v~~~  413 (787)
                      ..++|||+|||+++++++|+++|++||.|.+++|++| .+|+++|||||+|.+.++|++|++.||+..+. |+.|.|.++
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4579999999999999999999999999999999999 78999999999999999999999999998885 777777654


Q ss_pred             CCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCC-eeEEEec-------CCCcE
Q psy3345         414 KPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD-LGRVLVP-------PYGIT  485 (787)
Q Consensus       414 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~-v~~v~i~-------~~~~~  485 (787)
                      .                               ..++|+|.|||..+++++|.++|+.++. +..+.+.       .++++
T Consensus       136 ~-------------------------------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGF  184 (578)
T TIGR01648       136 V-------------------------------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGF  184 (578)
T ss_pred             c-------------------------------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCce
Confidence            3                               2478999999999999999999999864 4444432       24579


Q ss_pred             EEEEeCCHHHHHHHHHHhcC--CeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCc
Q psy3345         486 GLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVP  563 (787)
Q Consensus       486 a~V~F~~~~~A~~A~~~l~~--~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  563 (787)
                      |||+|.++++|..|+..|+.  ..+.|+.|.|+|+.+..-.                                       
T Consensus       185 AFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~---------------------------------------  225 (578)
T TIGR01648       185 AFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEV---------------------------------------  225 (578)
T ss_pred             EEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccc---------------------------------------
Confidence            99999999999999998864  3577999999999544100                                       


Q ss_pred             ccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhc--CCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHH
Q psy3345         564 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC--GPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN  641 (787)
Q Consensus       564 ~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~--G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~  641 (787)
                               ........++|||+|||.++++++|+++|++|  |.|.+|++++             +||||+|.+.++|.
T Consensus       226 ---------d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-------------gfAFVeF~s~e~A~  283 (578)
T TIGR01648       226 ---------DEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-------------DYAFVHFEDREDAV  283 (578)
T ss_pred             ---------cccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-------------CeEEEEeCCHHHHH
Confidence                     00112234789999999999999999999999  9999987653             69999999999999


Q ss_pred             HHHHHhCCCccCCeEEEEEecCccccchhh--------------hhhhccccccCCCCCEEEEecCCccCcHHHHHHHHH
Q psy3345         642 QALKVLQNSSLDEHQIELKRSNRNLESEAT--------------TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFK  707 (787)
Q Consensus       642 ~A~~~lng~~l~g~~l~v~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~  707 (787)
                      +|+..|||..|+|+.|.|.++.+.......              ...+............+++.|+++.++++-+.++|.
T Consensus       284 kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~  363 (578)
T TIGR01648       284 KAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPR  363 (578)
T ss_pred             HHHHHhCCCEECCEEEEEEEccCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchhhccc
Confidence            999999999999999999999764331000              000111122234678999999999999999999999


Q ss_pred             hcCCee
Q psy3345         708 AFGELK  713 (787)
Q Consensus       708 ~~G~I~  713 (787)
                      .+|.|.
T Consensus       364 ~~g~~~  369 (578)
T TIGR01648       364 MPGPIR  369 (578)
T ss_pred             cCcccc
Confidence            999764

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0110|consensus

Probab=100.00  E-value=3.3e-38  Score=334.79  Aligned_cols=426  Identities=24%  Similarity=0.330  Sum_probs=291.8

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ...+|+|||     |||++||+||+.+|                      |||+|..++.|.+|...+|++.++||.++|
T Consensus       226 etgrlf~RN-----Lpyt~~eed~~~lf----------------------a~v~~~~~~~avka~~~~D~k~fqgrmlhv  278 (725)
T KOG0110|consen  226 ETGRLFVRN-----LPYTSTEEDLLKLF----------------------AFVTFMFPEHAVKAYSELDGKVFQGRMLHV  278 (725)
T ss_pred             hhhhhhhcc-----CCccccHHHHHHhh----------------------HHHhhhhhHHHHhhhhhccccccccceeee
Confidence            467899999     99999999999999                      999999999999999999999999999999


Q ss_pred             EEccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchH------HHHHHhCCCcccCccC
Q psy3345          91 EKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFS------DFLQLHGKDVSKLLPL  164 (787)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~  164 (787)
                      .+..+.....  .   ..+.....++...+-          +++.....-..||+.++      ..|+...+..++ +.+
T Consensus       279 lp~~~k~~~~--~---~~~~~~~~~k~~ke~----------~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~-~i~  342 (725)
T KOG0110|consen  279 LPSKEKSTAK--E---DASELGSDYKKEKEL----------KRKAASASFHSWNTLFMGANAVAGILAQKLGVEKS-RIL  342 (725)
T ss_pred             cCcchhhhhh--h---hHhhcCCcHHHHHHh----------ccccchhcceecccccccccHHHHHHHHHhCCeee-eee
Confidence            9888622111  0   011111112222111          11112344567877776      455555554444 333


Q ss_pred             CCCCCCc-----cccccccccccccccCCCCcHHHHhhc-cC--CCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCC
Q psy3345         165 SNKDGEE-----KEEENEDESNNQIAHADISDMEYLKLK-TK--SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGV  236 (787)
Q Consensus       165 ~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~  236 (787)
                      +-.....     +.++.+..+.+          .++... |.  +++               ...++.+.|+++|||..+
T Consensus       343 d~~~~gsavr~al~etr~~~e~~----------~~~ee~gV~l~~F~---------------~~~rs~~vil~kNlpa~t  397 (725)
T KOG0110|consen  343 DGSLSGSAVRLALGETRVVQEVR----------RFFEENGVKLDAFS---------------QAERSDTVILVKNLPAGT  397 (725)
T ss_pred             chhhcchHHHHHHHHhhhchhhh----------hhHHhhCcccccch---------------hhhhhcceeeeccCcccc
Confidence            3211100     11111111111          222222 21  111               146788999999999999


Q ss_pred             CHHhHHHhhcCCCCc-ceeecccc-eEEEeecChHhHHHHHh-cCCcccCCeeEEEeecccCCccccCCCcCCCCchhhh
Q psy3345         237 KKKDLKAYFKPLPLA-SVRTTFLG-MAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASME  313 (787)
Q Consensus       237 te~di~~~F~~~g~v-~i~i~~~g-~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~  313 (787)
                      ..++|...|..||.+ .+.+++.| .|+|+|.++.+|++|+. +....+...++.+. |+|.+..............+..
T Consensus       398 ~~~elt~~F~~fG~i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle-~aP~dvf~~~pka~~~~~e~~~  476 (725)
T KOG0110|consen  398 LSEELTEAFLRFGEIGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLE-WAPEDVFTEDPKADDLSAESRS  476 (725)
T ss_pred             ccHHHHHHhhcccccceeecCcccceeeeeecCccchHHHHHHhchhhhccCccccc-cChhhhccCCcccccccccccc
Confidence            999999999999988 46555666 69999999999999999 66666666666552 3555544422111111110011


Q ss_pred             h----hhhccccc------ccc-----hhh-hhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCC--
Q psy3345         314 N----IKAKHWKS------QED-----SVQ-FAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--  375 (787)
Q Consensus       314 ~----~~~~~~~~------~~~-----~~~-~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~--  375 (787)
                      .    ........      ...     ... ........++|||+||++++|.++|..+|...|.|.++.|...++..  
T Consensus       477 ~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k  556 (725)
T KOG0110|consen  477 KMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANK  556 (725)
T ss_pred             ccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEecccccccc
Confidence            1    00000000      000     000 00111223349999999999999999999999999999887654321  


Q ss_pred             -CcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeC
Q psy3345         376 -KTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKN  454 (787)
Q Consensus       376 -~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~n  454 (787)
                       .+.|||||+|.++++|+.|++.|+|+.+.|+.|.|.++..+.....  +              .........+.|+|+|
T Consensus       557 ~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~--g--------------K~~~~kk~~tKIlVRN  620 (725)
T KOG0110|consen  557 YLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTV--G--------------KKKSKKKKGTKILVRN  620 (725)
T ss_pred             ccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCcccccc--c--------------cccccccccceeeeec
Confidence             2679999999999999999999999999999999999872211100  0              0111223367999999


Q ss_pred             CCCCCCHHHHHHhhccCCCeeEEEecCC------CcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCc
Q psy3345         455 LPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  521 (787)
Q Consensus       455 lp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~  521 (787)
                      ||+.++..+++.+|..||.|.+|.||..      .|+|||.|.++.+|.+|+.+|.+++++||.|.++|+...
T Consensus       621 ipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  621 IPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             cchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccc
Confidence            9999999999999999999999999974      468999999999999999999999999999999999766

>KOG0123|consensus

Probab=100.00  E-value=1.1e-36  Score=320.48  Aligned_cols=338  Identities=25%  Similarity=0.390  Sum_probs=281.9

Q ss_pred             eEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec----ccceEEEeecChHhHHHHHh-cCCcccCCeeEEEeecccCCccc
Q psy3345         226 TIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT----FLGMAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYSKDNSAK  299 (787)
Q Consensus       226 ~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~----~~g~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~~~~~~~  299 (787)
                      .|||+   +++|+..|.++|++.|.+ +++++    +.|+|||.|.++++|.+|+. +|...+.|++|.|          
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~ri----------   69 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRI----------   69 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEe----------
Confidence            57888   899999999999999988 88888    55899999999999999999 8999999999999          


Q ss_pred             cCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcce
Q psy3345         300 YSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG  379 (787)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g  379 (787)
                                         .|+...           ...|||.||+.+++..+|.++|+.||.|++|++..+.. | ++|
T Consensus        70 -------------------m~s~rd-----------~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg  117 (369)
T KOG0123|consen   70 -------------------MWSQRD-----------PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKG  117 (369)
T ss_pred             -------------------ehhccC-----------CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-cee
Confidence                               443211           11299999999999999999999999999999999854 5 999


Q ss_pred             EEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCC
Q psy3345         380 FALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRT  459 (787)
Q Consensus       380 ~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~  459 (787)
                      | ||+|.+++.|.+|++.+||..+.|+.|.|.....++.....                ... .....+.++++|++.+.
T Consensus       118 ~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~----------------~~~-~~~~~t~v~vk~~~~~~  179 (369)
T KOG0123|consen  118 Y-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAP----------------LGE-YKKRFTNVYVKNLEEDS  179 (369)
T ss_pred             e-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhccc----------------ccc-hhhhhhhhheecccccc
Confidence            9 99999999999999999999999999999988876221100                011 23446789999999999


Q ss_pred             CHHHHHHhhccCCCeeEEEecC-----CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCcccccccccccccc
Q psy3345         460 LPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKE  534 (787)
Q Consensus       460 t~~~l~~~F~~~G~v~~v~i~~-----~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~  534 (787)
                      +.+.|..+|+.+|.|.++.+.+     +++++||+|.++++|..|+..|++..+.+..++|..+....-...        
T Consensus       180 ~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~--------  251 (369)
T KOG0123|consen  180 TDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREA--------  251 (369)
T ss_pred             chHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHH--------
Confidence            9999999999999999998876     357999999999999999999999999999999987754210000        


Q ss_pred             ccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEee
Q psy3345         535 KEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  614 (787)
Q Consensus       535 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~  614 (787)
                            ...            .         ................+|||+|++..++.+.|+.+|+.||.|.+++|..
T Consensus       252 ------~l~------------~---------~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~  304 (369)
T KOG0123|consen  252 ------ELK------------R---------KFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMV  304 (369)
T ss_pred             ------HHh------------h---------hhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEe
Confidence                  000            0         0000001122345678999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCcccc
Q psy3345         615 KKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE  667 (787)
Q Consensus       615 ~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~  667 (787)
                      +..      +.++|||||+|.+.++|.+|+..+||..++|+.|.|.+..+...
T Consensus       305 ~~~------g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~  351 (369)
T KOG0123|consen  305 DEN------GKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKED  351 (369)
T ss_pred             ccC------CCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhcc
Confidence            875      78999999999999999999999999999999999988774433

>KOG0145|consensus

Probab=100.00  E-value=2.1e-36  Score=282.01  Aligned_cols=263  Identities=23%  Similarity=0.347  Sum_probs=228.4

Q ss_pred             cCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCC------cEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEE
Q psy3345         444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG------ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  517 (787)
Q Consensus       444 ~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~------~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  517 (787)
                      ..+.+.|+|.-||..+|.++++.+|...|+|++|++.+++      |++||.|.++++|++|+..|||-++..++|.|.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            4567899999999999999999999999999999998755      6899999999999999999999999999999999


Q ss_pred             ecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHH
Q psy3345         518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSI  597 (787)
Q Consensus       518 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L  597 (787)
                      +.+.                                                     .......+|||.+||.++|..+|
T Consensus       118 ARPS-----------------------------------------------------s~~Ik~aNLYvSGlPktMtqkel  144 (360)
T KOG0145|consen  118 ARPS-----------------------------------------------------SDSIKDANLYVSGLPKTMTQKEL  144 (360)
T ss_pred             ccCC-----------------------------------------------------hhhhcccceEEecCCccchHHHH
Confidence            9554                                                     12334678999999999999999


Q ss_pred             HHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC--eEEEEEecCccccchhh----
Q psy3345         598 RRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDE--HQIELKRSNRNLESEAT----  671 (787)
Q Consensus       598 ~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g--~~l~v~~~~~~~~~~~~----  671 (787)
                      ..+|++||.|...+|+.|.-     ++.++|.|||.|....+|.+|++.|||..-.|  .+|.|+|+.........    
T Consensus       145 E~iFs~fGrIItSRiL~dqv-----tg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls  219 (360)
T KOG0145|consen  145 EQIFSPFGRIITSRILVDQV-----TGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLS  219 (360)
T ss_pred             HHHHHHhhhhhhhhhhhhcc-----cceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhH
Confidence            99999999999999998765     78999999999999999999999999998877  58999998754321000    


Q ss_pred             ----------------hhh---------------hc--------------cccccCCCCCEEEEecCCccCcHHHHHHHH
Q psy3345         672 ----------------TVK---------------RK--------------SSNVAKQTGSKILVRNIPFQAKQSEVEELF  706 (787)
Q Consensus       672 ----------------~~~---------------~~--------------~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F  706 (787)
                                      ..+               +.              ..+.....+++|||.||.+++++.-|.++|
T Consensus       220 ~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlF  299 (360)
T KOG0145|consen  220 QLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLF  299 (360)
T ss_pred             HhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHh
Confidence                            000               00              001112357999999999999999999999


Q ss_pred             HhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccc
Q psy3345         707 KAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE  766 (787)
Q Consensus       707 ~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~  766 (787)
                      ++||.|..|+|++|+ .+.+++|||||.+.+.++|..||..|| |..+.+|.|.|+|...
T Consensus       300 gpFGAv~nVKvirD~-ttnkCKGfgFVtMtNYdEAamAi~sLN-Gy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  300 GPFGAVTNVKVIRDF-TTNKCKGFGFVTMTNYDEAAMAIASLN-GYRLGDRVLQVSFKTN  357 (360)
T ss_pred             CcccceeeEEEEecC-CcccccceeEEEecchHHHHHHHHHhc-CccccceEEEEEEecC
Confidence            999999999999998 679999999999999999999999997 7999999999999753

>KOG0117|consensus

Probab=100.00  E-value=8.8e-36  Score=299.24  Aligned_cols=254  Identities=25%  Similarity=0.411  Sum_probs=219.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee-CCeEEEEee
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF-LGRMLHLIP  412 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~-~g~~l~v~~  412 (787)
                      ..++-|||+.||.++.|++|..+|++.|+|.++++++|+.+|.++|||||.|.+.++|+.|++.||+..| .|+.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            5678899999999999999999999999999999999999999999999999999999999999998766 345544432


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCC
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQ  492 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~  492 (787)
                      +.                                                                              
T Consensus       161 Sv------------------------------------------------------------------------------  162 (506)
T KOG0117|consen  161 SV------------------------------------------------------------------------------  162 (506)
T ss_pred             ee------------------------------------------------------------------------------
Confidence            11                                                                              


Q ss_pred             HHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccc
Q psy3345         493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEED  572 (787)
Q Consensus       493 ~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  572 (787)
                                                                                                      
T Consensus       163 --------------------------------------------------------------------------------  162 (506)
T KOG0117|consen  163 --------------------------------------------------------------------------------  162 (506)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             cccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCC-eEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCC--
Q psy3345         573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQN--  649 (787)
Q Consensus       573 ~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~-v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng--  649 (787)
                            ..++|||+|||.++++++|++.|++.++ |.+|.+...++    .+.+++|||||+|.++..|..|.+.|-.  
T Consensus       163 ------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~----dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~  232 (506)
T KOG0117|consen  163 ------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPD----DKTKNRGFAFVEYESHRAAAMARRKLMPGK  232 (506)
T ss_pred             ------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCcc----ccccccceEEEEeecchhHHHHHhhccCCc
Confidence                  1478999999999999999999999875 78888776654    4678999999999999999999988743  


Q ss_pred             CccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCce
Q psy3345         650 SSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG  729 (787)
Q Consensus       650 ~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g  729 (787)
                      ..+.|+.+.|.|+.+.........         ..-..|||+||+.++|++.|+++|+.||.|..|+.++|         
T Consensus       233 ~klwgn~~tVdWAep~~e~ded~m---------s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD---------  294 (506)
T KOG0117|consen  233 IKLWGNAITVDWAEPEEEPDEDTM---------SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD---------  294 (506)
T ss_pred             eeecCCcceeeccCcccCCChhhh---------hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc---------
Confidence            567999999999987766322211         12457999999999999999999999999999988877         


Q ss_pred             EEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccccHHHHH
Q psy3345         730 FGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIR  774 (787)
Q Consensus       730 ~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~~~~~  774 (787)
                      ||||.|.+.++|.+||+.+| ++.|.|..|.|.+|+|.+.....|
T Consensus       295 YaFVHf~eR~davkAm~~~n-gkeldG~~iEvtLAKP~~k~k~~r  338 (506)
T KOG0117|consen  295 YAFVHFAEREDAVKAMKETN-GKELDGSPIEVTLAKPVDKKKKER  338 (506)
T ss_pred             eeEEeecchHHHHHHHHHhc-CceecCceEEEEecCChhhhccch
Confidence            89999999999999999997 799999999999999888654443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=100.00  E-value=1.2e-34  Score=318.18  Aligned_cols=282  Identities=20%  Similarity=0.252  Sum_probs=225.7

Q ss_pred             CHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHH
Q psy3345         387 MPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKA  466 (787)
Q Consensus       387 ~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~  466 (787)
                      ..+.|.+||..++|..+........+..+....                    ........+.|||.|||.++++++|.+
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~--------------------~~~~p~~~~~lFVgnLp~~~tEd~L~~   77 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGW--------------------SGVQPGRGCEVFVGKIPRDLYEDELVP   77 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCcc--------------------cCCCCCCCCEEEeCCCCCCCCHHHHHH
Confidence            368899999888988776655555554332100                    011223468999999999999999999


Q ss_pred             hhccCCCeeEEEecC-----CCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeeEEEEEecCcccccccccccccccccccc
Q psy3345         467 LFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAPEGVFAEAKEKSKGKEKEKNEE  540 (787)
Q Consensus       467 ~F~~~G~v~~v~i~~-----~~~~a~V~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~  540 (787)
                      +|++||.|..+.|..     ++++|||+|.+.++|.+|++.|++..+. |+.|.|.++.                     
T Consensus        78 ~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~---------------------  136 (578)
T TIGR01648        78 LFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV---------------------  136 (578)
T ss_pred             HHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc---------------------
Confidence            999999999888753     5579999999999999999999998886 6766665431                     


Q ss_pred             ccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCC-eEEEEEeecCCCC
Q psy3345         541 EGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPK  619 (787)
Q Consensus       541 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~-v~~v~i~~~~~~~  619 (787)
                                                            ..++|||+|||+++++++|.+.|++++. +..+.+....   
T Consensus       137 --------------------------------------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~---  175 (578)
T TIGR01648       137 --------------------------------------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSA---  175 (578)
T ss_pred             --------------------------------------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccc---
Confidence                                                  2478999999999999999999999864 5554443222   


Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCC--CccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccC
Q psy3345         620 SPGQFLSMGYGFVQFYTRESLNQALKVLQN--SSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA  697 (787)
Q Consensus       620 ~~~~~~s~G~afV~F~~~e~A~~A~~~lng--~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~  697 (787)
                       ..++.++|||||+|.++++|..|+..|+.  ..+.|+.|.|.|+.+.....         .......++|||+|||..+
T Consensus       176 -~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d---------~~~~~~~k~LfVgNL~~~~  245 (578)
T TIGR01648       176 -ADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVD---------EDVMAKVKILYVRNLMTTT  245 (578)
T ss_pred             -cccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccc---------ccccccccEEEEeCCCCCC
Confidence             12457899999999999999999998864  35789999999987654311         1112345789999999999


Q ss_pred             cHHHHHHHHHhc--CCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccccH
Q psy3345         698 KQSEVEELFKAF--GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNV  770 (787)
Q Consensus       698 t~~dL~~~F~~~--G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~  770 (787)
                      |+++|+++|+.|  |.|..|++++         +||||+|.+.++|.+||..|| +..|.|+.|.|+||+|.+..
T Consensus       246 tee~L~~~F~~f~~G~I~rV~~~r---------gfAFVeF~s~e~A~kAi~~ln-G~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       246 TEEIIEKSFSEFKPGKVERVKKIR---------DYAFVHFEDREDAVKAMDELN-GKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             CHHHHHHHHHhcCCCceEEEEeec---------CeEEEEeCCHHHHHHHHHHhC-CCEECCEEEEEEEccCCCcc
Confidence            999999999999  9999997743         589999999999999999997 79999999999999987654

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0145|consensus

Probab=100.00  E-value=3.2e-34  Score=267.45  Aligned_cols=300  Identities=19%  Similarity=0.316  Sum_probs=226.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      ..+.|.|.-||..+|+++|+.+|+..|+|++|++++|+-+|.+.||+||.|-+++||.+|+..|||..++.++|+|.++.
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCee--EEEecC----CCcEEEE
Q psy3345         415 PKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLG--RVLVPP----YGITGLV  488 (787)
Q Consensus       415 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~--~v~i~~----~~~~a~V  488 (787)
                      +..                         .......|||.+||..+|..||.++|++||.|.  +|.++.    ++|.+||
T Consensus       120 PSs-------------------------~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFi  174 (360)
T KOG0145|consen  120 PSS-------------------------DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFI  174 (360)
T ss_pred             CCh-------------------------hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEE
Confidence            651                         223457899999999999999999999999985  344433    5678999


Q ss_pred             EeCCHHHHHHHHHHhcCCeeCC--eeEEEEEecCcccccccc-ccccccccc---cccccccchhhhhcccccccc--cC
Q psy3345         489 EFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEGVFAEAKE-KSKGKEKEK---NEEEGEEGEEEKKENTAEEDN--QQ  560 (787)
Q Consensus       489 ~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~~~~~~~~~~~~-~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~--~~  560 (787)
                      .|....+|..|+..|||..-.|  .+|.|.|+....-..... -...-+.+.   ..+.....+.-+-+.......  ..
T Consensus       175 RFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~r  254 (360)
T KOG0145|consen  175 RFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQAR  254 (360)
T ss_pred             EecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhcc
Confidence            9999999999999999988776  478998874331000000 000000000   000000000000000000000  00


Q ss_pred             CCccccccc----ccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCC
Q psy3345         561 GVPEVEENV----EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT  636 (787)
Q Consensus       561 ~~~~~~~~~----~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~  636 (787)
                      .++-.....    .-..+.....+.+|||.||.+++++.-|+++|.+||.|.+|++++|..     +...+|||||.+.+
T Consensus       255 fsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~t-----tnkCKGfgFVtMtN  329 (360)
T KOG0145|consen  255 FSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFT-----TNKCKGFGFVTMTN  329 (360)
T ss_pred             CCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCC-----cccccceeEEEecc
Confidence            000000000    001133455578999999999999999999999999999999999987     67899999999999


Q ss_pred             HHHHHHHHHHhCCCccCCeEEEEEecCc
Q psy3345         637 RESLNQALKVLQNSSLDEHQIELKRSNR  664 (787)
Q Consensus       637 ~e~A~~A~~~lng~~l~g~~l~v~~~~~  664 (787)
                      -++|..|+..|||..++++.|.|.|...
T Consensus       330 YdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  330 YDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             hHHHHHHHHHhcCccccceEEEEEEecC
Confidence            9999999999999999999999998654

>KOG0117|consensus

Probab=100.00  E-value=8.2e-33  Score=277.95  Aligned_cols=234  Identities=23%  Similarity=0.379  Sum_probs=199.0

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccC-CceEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVF-SSRIK   89 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~-~~~i~   89 (787)
                      ..-|+|-+     ||.++.|+||..||.+.|.|.+++|++++ +|.+||||||+|.+.++|++||+.||+..|. |+.|.
T Consensus        83 G~EVfvGk-----IPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~ig  157 (506)
T KOG0117|consen   83 GCEVFVGK-----IPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLG  157 (506)
T ss_pred             CceEEecC-----CCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeE
Confidence            45699999     99999999999999999999999999997 8999999999999999999999999999774 56666


Q ss_pred             EEEccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCC
Q psy3345          90 VEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDG  169 (787)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (787)
                      |..+.                                                                           
T Consensus       158 vc~Sv---------------------------------------------------------------------------  162 (506)
T KOG0117|consen  158 VCVSV---------------------------------------------------------------------------  162 (506)
T ss_pred             EEEee---------------------------------------------------------------------------
Confidence            64432                                                                           


Q ss_pred             CccccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCC-
Q psy3345         170 EEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-  248 (787)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~-  248 (787)
                                                                           .+++|||+|||.+.++++|.+-|+.. 
T Consensus       163 -----------------------------------------------------an~RLFiG~IPK~k~keeIlee~~kVt  189 (506)
T KOG0117|consen  163 -----------------------------------------------------ANCRLFIGNIPKTKKKEEILEEMKKVT  189 (506)
T ss_pred             -----------------------------------------------------ecceeEeccCCccccHHHHHHHHHhhC
Confidence                                                                 36789999999999999999999999 


Q ss_pred             -CCcceeec--------ccceEEEeecChHhHHHHHhc--C-CcccCCeeEEEeecccCCccccCCCcCCCCchhhhhhh
Q psy3345         249 -PLASVRTT--------FLGMAYIGFKDEKNCNKALNK--N-KSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIK  316 (787)
Q Consensus       249 -g~v~i~i~--------~~g~afV~F~~~~~A~~Al~~--~-~~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~  316 (787)
                       |+++|.+.        ++|+|||+|.+...|..|-.+  . +..+-|..+.|                           
T Consensus       190 eGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tV---------------------------  242 (506)
T KOG0117|consen  190 EGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITV---------------------------  242 (506)
T ss_pred             CCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCccee---------------------------
Confidence             56676666        679999999999999888872  2 45567777777                           


Q ss_pred             hcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHH
Q psy3345         317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ  396 (787)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~  396 (787)
                        .|.....+.+.+ .......|||+||+.++|++.|+++|+.||.|..|..++|        ||||.|.+.++|.+|++
T Consensus       243 --dWAep~~e~ded-~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~  311 (506)
T KOG0117|consen  243 --DWAEPEEEPDED-TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMK  311 (506)
T ss_pred             --eccCcccCCChh-hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHH
Confidence              332211111111 2333457999999999999999999999999999988765        99999999999999999


Q ss_pred             HhCCceeCCeEEEEeeCCCC
Q psy3345         397 HLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       397 ~l~~~~~~g~~l~v~~~~~~  416 (787)
                      .+||..|.|..|.|.++++.
T Consensus       312 ~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  312 ETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             HhcCceecCceEEEEecCCh
Confidence            99999999999999999987

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=100.00  E-value=3.5e-32  Score=309.68  Aligned_cols=294  Identities=16%  Similarity=0.249  Sum_probs=218.5

Q ss_pred             hcCCCCEEEEeCCCCCCCHHHHHHhhccC------------CCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC
Q psy3345         443 EARSKRIILVKNLPYRTLPTDLKALFEPF------------GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE  510 (787)
Q Consensus       443 ~~~~~~~i~v~nlp~~~t~~~l~~~F~~~------------G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g  510 (787)
                      ......+|||+|||+.+|+++|.++|..+            +.|..+.+..++++|||+|.+.++|..|+ .|+|..|.|
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~~~g  249 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAM-ALDSIIYSN  249 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhh-cCCCeEeeC
Confidence            34556899999999999999999999874            45677888889999999999999999999 599999999


Q ss_pred             eeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCC
Q psy3345         511 VPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNF  590 (787)
Q Consensus       511 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~  590 (787)
                      ++|.|.+....  ...........     ...+       ......          ..............++|||+|||+
T Consensus       250 ~~l~v~r~~~~--~~~~~~~~~~~-----~~~~-------~~~~~~----------~~~~~~~~~~~~~~~~l~v~nlp~  305 (509)
T TIGR01642       250 VFLKIRRPHDY--IPVPQITPEVS-----QKNP-------DDNAKN----------VEKLVNSTTVLDSKDRIYIGNLPL  305 (509)
T ss_pred             ceeEecCcccc--CCccccCCCCC-----CCCC-------cccccc----------cccccccccCCCCCCEEEEeCCCC
Confidence            99998754221  10000000000     0000       000000          000000011234568999999999


Q ss_pred             CCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchh
Q psy3345         591 NSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA  670 (787)
Q Consensus       591 ~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~  670 (787)
                      .+++++|.++|+.||.|..+.++++..     ++.++|||||+|.+.++|..|+..|||..|+|+.|.|.++........
T Consensus       306 ~~~~~~l~~~f~~~G~i~~~~~~~~~~-----~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~  380 (509)
T TIGR01642       306 YLGEDQIKELLESFGDLKAFNLIKDIA-----TGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQAT  380 (509)
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEEecCC-----CCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCC
Confidence            999999999999999999999998765     678999999999999999999999999999999999999864322110


Q ss_pred             hh--------------hhhccccccCCCCCEEEEecCCccC----------cHHHHHHHHHhcCCeeEEEecccc--CCC
Q psy3345         671 TT--------------VKRKSSNVAKQTGSKILVRNIPFQA----------KQSEVEELFKAFGELKFVRLPKKM--VGS  724 (787)
Q Consensus       671 ~~--------------~~~~~~~~~~~~~~~l~V~nLp~~~----------t~~dL~~~F~~~G~I~~v~i~~~~--~~~  724 (787)
                      ..              ...........+..+|+|.||....          ..++|+++|++||.|.+|.|++..  ..+
T Consensus       381 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~  460 (509)
T TIGR01642       381 IDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNS  460 (509)
T ss_pred             ccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCc
Confidence            00              0000001123467889999996431          236899999999999999998762  123


Q ss_pred             CCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccc
Q psy3345         725 GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEA  767 (787)
Q Consensus       725 g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~  767 (787)
                      +...|+|||+|.+.++|.+|+..|| |+.|.|+.|.|.|..++
T Consensus       461 ~~~~G~~fV~F~~~e~A~~A~~~ln-Gr~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       461 TPGVGKVFLEYADVRSAEKAMEGMN-GRKFNDRVVVAAFYGED  502 (509)
T ss_pred             CCCcceEEEEECCHHHHHHHHHHcC-CCEECCeEEEEEEeCHH
Confidence            5567999999999999999999997 79999999999998754

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=100.00  E-value=4.7e-32  Score=308.60  Aligned_cols=300  Identities=18%  Similarity=0.277  Sum_probs=214.3

Q ss_pred             cCCCccceEEEeCCCCCCCHHhHHHhhcCC------------CCc-ceeec-ccceEEEeecChHhHHHHHhcCCcccCC
Q psy3345         219 VHKRQYHTIVVKNLPAGVKKKDLKAYFKPL------------PLA-SVRTT-FLGMAYIGFKDEKNCNKALNKNKSFWKG  284 (787)
Q Consensus       219 ~~~~~~~~v~v~nLp~~~te~di~~~F~~~------------g~v-~i~i~-~~g~afV~F~~~~~A~~Al~~~~~~l~g  284 (787)
                      ...+..++|||+|||+++|+++|.+||..+            +.+ .+.+. .+|+|||+|.+.++|..||.+++..+.|
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g  249 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYSN  249 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeC
Confidence            345677899999999999999999999874            122 23333 6799999999999999999999999999


Q ss_pred             eeEEEeecccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee
Q psy3345         285 KQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLA  364 (787)
Q Consensus       285 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~  364 (787)
                      +.|.|..  +......+.......    .......+................++|||+|||+.+|+++|+++|+.||.|.
T Consensus       250 ~~l~v~r--~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~  323 (509)
T TIGR01642       250 VFLKIRR--PHDYIPVPQITPEVS----QKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLK  323 (509)
T ss_pred             ceeEecC--ccccCCccccCCCCC----CCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCee
Confidence            9999852  111110000000000    0000000000000001111234567999999999999999999999999999


Q ss_pred             EEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCC---ccccccccccchhhhh
Q psy3345         365 EVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGK---VHCCISERKLDAFNQV  441 (787)
Q Consensus       365 ~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~---~~~a~~~~~~~~~~~~  441 (787)
                      .+.++.+..+|.++|||||+|.+.++|..|+..|+|..|.|+.|.|.++............   .........+......
T Consensus       324 ~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (509)
T TIGR01642       324 AFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQ  403 (509)
T ss_pred             EEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhcc
Confidence            9999999889999999999999999999999999999999999999998654211110000   0000000000000001


Q ss_pred             hhcCCCCEEEEeCCCCCC----------CHHHHHHhhccCCCeeEEEecCC---------CcEEEEEeCCHHHHHHHHHH
Q psy3345         442 VEARSKRIILVKNLPYRT----------LPTDLKALFEPFGDLGRVLVPPY---------GITGLVEFLQKNQAKAAFNS  502 (787)
Q Consensus       442 ~~~~~~~~i~v~nlp~~~----------t~~~l~~~F~~~G~v~~v~i~~~---------~~~a~V~F~~~~~A~~A~~~  502 (787)
                      ....+..+|+|.|+...-          ..++|+++|++||.|..|.|+..         .|+|||+|.+.++|.+|+..
T Consensus       404 ~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~  483 (509)
T TIGR01642       404 IGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEG  483 (509)
T ss_pred             ccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHH
Confidence            123457889999996431          23689999999999999999752         36899999999999999999


Q ss_pred             hcCCeeCCeeEEEEEecCcccc
Q psy3345         503 LAYTKFKEVPLYLEWAPEGVFA  524 (787)
Q Consensus       503 l~~~~~~g~~l~v~~~~~~~~~  524 (787)
                      |||+.|.|+.|.+.|.+...|.
T Consensus       484 lnGr~~~gr~v~~~~~~~~~~~  505 (509)
T TIGR01642       484 MNGRKFNDRVVVAAFYGEDCYK  505 (509)
T ss_pred             cCCCEECCeEEEEEEeCHHHhh
Confidence            9999999999999999877553

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=100.00  E-value=2.4e-31  Score=298.31  Aligned_cols=308  Identities=20%  Similarity=0.305  Sum_probs=218.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ...++|||+|||+.+++++|+++|+.||.|.+|.++.++.+|+++|||||+|.+.++|.+|+. |+|..+.|++|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            456799999999999999999999999999999999999999999999999999999999996 9999999999999876


Q ss_pred             CCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC------CCcEEE
Q psy3345         414 KPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGL  487 (787)
Q Consensus       414 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~------~~~~a~  487 (787)
                      ........     ..+.        ......+...+|+|.|||..+++++|.++|+.||.|..|.+..      ..++||
T Consensus       166 ~~~~~~~~-----~~~~--------~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~af  232 (457)
T TIGR01622       166 QAEKNRAA-----KAAT--------HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGF  232 (457)
T ss_pred             chhhhhhh-----hccc--------ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEE
Confidence            54311100     0000        0001122368999999999999999999999999999988874      347999


Q ss_pred             EEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCcccccccccccccccc--cccccc-ccchh-hhhcccccc-------
Q psy3345         488 VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKE--KNEEEG-EEGEE-EKKENTAEE-------  556 (787)
Q Consensus       488 V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~--~~~~~~-~~~~~-~~~~~~~~~-------  556 (787)
                      |+|.+.++|..|+..|+|..+.|++|.|.|+..................  ...... ..... .........       
T Consensus       233 V~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  312 (457)
T TIGR01622       233 IQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLI  312 (457)
T ss_pred             EEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccC
Confidence            9999999999999999999999999999997533211111000000000  000000 00000 000000000       


Q ss_pred             -----------cccCC------Cc---cccc----cccc--ccccCCCCCCeEEecCCCCCCC----------HHHHHHH
Q psy3345         557 -----------DNQQG------VP---EVEE----NVEE--DEEREPEPDTTLYIKNLNFNST----------EDSIRRH  600 (787)
Q Consensus       557 -----------~~~~~------~~---~~~~----~~~~--~~~~~~~~~~~l~V~NLp~~~t----------~~~L~~~  600 (787)
                                 .....      .+   ....    ....  .......+..+|+|.||....+          .++|++.
T Consensus       313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e  392 (457)
T TIGR01622       313 PGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEE  392 (457)
T ss_pred             CCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHH
Confidence                       00000      00   0000    0000  0011335678999999955544          3679999


Q ss_pred             HhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCc
Q psy3345         601 FKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR  664 (787)
Q Consensus       601 F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~  664 (787)
                      |++||.|..+.|...         .+.|++||+|.++++|..|++.|||..++|+.|.+.+...
T Consensus       393 ~~k~G~v~~v~v~~~---------~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       393 CSKYGGVVHIYVDTK---------NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             HHhcCCeeEEEEeCC---------CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            999999999998742         3569999999999999999999999999999999998753

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=100.00  E-value=2e-31  Score=298.92  Aligned_cols=271  Identities=21%  Similarity=0.282  Sum_probs=214.0

Q ss_pred             cCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC------CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEE
Q psy3345         444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  517 (787)
Q Consensus       444 ~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~------~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  517 (787)
                      .....+|||.|||..+++++|.++|+.||.|..|.+..      .+++|||+|.+.++|.+|+. |+|..+.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            34568999999999999999999999999999999865      35799999999999999996 999999999999987


Q ss_pred             ecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHH
Q psy3345         518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSI  597 (787)
Q Consensus       518 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L  597 (787)
                      .....-.....                          ..               .........++|||+|||+.+++++|
T Consensus       165 ~~~~~~~~~~~--------------------------~~---------------~~~~~~p~~~~l~v~nl~~~~te~~l  203 (457)
T TIGR01622       165 SQAEKNRAAKA--------------------------AT---------------HQPGDIPNFLKLYVGNLHFNITEQEL  203 (457)
T ss_pred             cchhhhhhhhc--------------------------cc---------------ccCCCCCCCCEEEEcCCCCCCCHHHH
Confidence            63321000000                          00               00001122689999999999999999


Q ss_pred             HHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchh-------
Q psy3345         598 RRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA-------  670 (787)
Q Consensus       598 ~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~-------  670 (787)
                      +++|++||.|..|.+..+..     ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++........       
T Consensus       204 ~~~f~~~G~i~~v~~~~d~~-----~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~  278 (457)
T TIGR01622       204 RQIFEPFGDIEDVQLHRDPE-----TGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFED  278 (457)
T ss_pred             HHHHHhcCCeEEEEEEEcCC-----CCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhcc
Confidence            99999999999999998765     568999999999999999999999999999999999999642110000       


Q ss_pred             -----------------hh---------------------------hhh-----------------------ccccc--c
Q psy3345         671 -----------------TT---------------------------VKR-----------------------KSSNV--A  681 (787)
Q Consensus       671 -----------------~~---------------------------~~~-----------------------~~~~~--~  681 (787)
                                       ..                           ...                       .....  .
T Consensus       279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  358 (457)
T TIGR01622       279 IDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNN  358 (457)
T ss_pred             ccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccC
Confidence                             00                           000                       00000  1


Q ss_pred             CCCCCEEEEecCCccCc----------HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCC
Q psy3345         682 KQTGSKILVRNIPFQAK----------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS  751 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t----------~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~  751 (787)
                      ..+..+|+|.||....+          .+||++.|++||.|..|.|...     ...|++||.|.+.++|.+|++.|| |
T Consensus       359 ~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~-----~~~G~~fV~F~~~e~A~~A~~~ln-G  432 (457)
T TIGR01622       359 NLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK-----NSAGKIYLKFSSVDAALAAFQALN-G  432 (457)
T ss_pred             CCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC-----CCceeEEEEECCHHHHHHHHHHhc-C
Confidence            24678999999955444          3689999999999999999644     257999999999999999999997 7


Q ss_pred             eeecCceEEEEEcccc
Q psy3345         752 THLYGRRLVLEWAEEA  767 (787)
Q Consensus       752 ~~~~Gr~l~v~~A~~~  767 (787)
                      +.|.||.|.+.|..++
T Consensus       433 r~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       433 RYFGGKMITAAFVVND  448 (457)
T ss_pred             cccCCeEEEEEEEcHH
Confidence            9999999999998744

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.98  E-value=1.3e-30  Score=286.24  Aligned_cols=80  Identities=18%  Similarity=0.320  Sum_probs=76.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      ++|||+|||+++++++|+++|+.||.|.++++.+++.+|+++|||||+|.+.++|.+|++.||+..++|+.|+|.++...
T Consensus       205 ~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             ceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            47999999999999999999999999999999999888999999999999999999999999999999999999987753

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148|consensus

Probab=99.97  E-value=3.3e-31  Score=249.57  Aligned_cols=234  Identities=23%  Similarity=0.327  Sum_probs=190.3

Q ss_pred             CccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeecccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecccCCcccc
Q psy3345         222 RQYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKY  300 (787)
Q Consensus       222 ~~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~~~~~~~~  300 (787)
                      ...++|||+||..++||+-|..+|+.+|.+ ..+++        |.                   .|.|           
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i--------~~-------------------e~~v-----------   45 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVI--------FD-------------------ELKV-----------   45 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceee--------hh-------------------hhcc-----------
Confidence            457899999999999999999999999998 44443        11                   1222           


Q ss_pred             CCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceE
Q psy3345         301 SGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF  380 (787)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~  380 (787)
                                        .|.-.+ .............|||+.|...++.++|++.|.+||+|.+++|++|..|++++||
T Consensus        46 ------------------~wa~~p-~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGY  106 (321)
T KOG0148|consen   46 ------------------NWATAP-GNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGY  106 (321)
T ss_pred             ------------------ccccCc-ccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccce
Confidence                              110000 0001112222457999999999999999999999999999999999999999999


Q ss_pred             EEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCC
Q psy3345         381 ALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTL  460 (787)
Q Consensus       381 afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t  460 (787)
                      +||.|.+.++|++||..|||.+|++|.|+..|+..+.....  +. ...-.+    .  .......+++|+|.|++..++
T Consensus       107 gFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n--~~-~ltfde----V--~NQssp~NtsVY~G~I~~~lt  177 (321)
T KOG0148|consen  107 GFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMN--GK-PLTFDE----V--YNQSSPDNTSVYVGNIASGLT  177 (321)
T ss_pred             eEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccC--CC-CccHHH----H--hccCCCCCceEEeCCcCcccc
Confidence            99999999999999999999999999999999997731111  00 000000    0  112456789999999999999


Q ss_pred             HHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCc
Q psy3345         461 PTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  521 (787)
Q Consensus       461 ~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~  521 (787)
                      +++|++.|++||.|..|++.+++++|||.|.+.|.|.+||..+|++.+.|..+++.|....
T Consensus       178 e~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  178 EDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             HHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            9999999999999999999999999999999999999999999999999999999999766

>KOG0148|consensus

Probab=99.97  E-value=3.5e-31  Score=249.45  Aligned_cols=234  Identities=22%  Similarity=0.371  Sum_probs=194.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccc
Q psy3345         446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE  525 (787)
Q Consensus       446 ~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~  525 (787)
                      ..++|+|.||..++|++-|..||++.|.|.++++..+                             .|.|.|+....   
T Consensus         5 ~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-----------------------------e~~v~wa~~p~---   52 (321)
T KOG0148|consen    5 EPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-----------------------------ELKVNWATAPG---   52 (321)
T ss_pred             CCceEEeeccChhhHHHHHHHHHHhccccccceeehh-----------------------------hhccccccCcc---
Confidence            3578999999999999999999999999988877633                             34555553220   


Q ss_pred             cccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcC
Q psy3345         526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCG  605 (787)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G  605 (787)
                        .+                                           .......-..+||+.|.+.++.+.|++.|.+||
T Consensus        53 --nQ-------------------------------------------sk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFG   87 (321)
T KOG0148|consen   53 --NQ-------------------------------------------SKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFG   87 (321)
T ss_pred             --cC-------------------------------------------CCCccccceeEEehhcchhcchHHHHHHhcccc
Confidence              00                                           000111235799999999999999999999999


Q ss_pred             CeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhh--hhhccccccCC
Q psy3345         606 PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT--VKRKSSNVAKQ  683 (787)
Q Consensus       606 ~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~--~~~~~~~~~~~  683 (787)
                      .|.+++|++|..     ++.|+|||||.|.+.++|+.||..|||..|++|.|+-.|+.++.......  ....-..+...
T Consensus        88 evS~akvirD~~-----T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp  162 (321)
T KOG0148|consen   88 EVSDAKVIRDMN-----TGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSP  162 (321)
T ss_pred             ccccceEeeccc-----CCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCC
Confidence            999999999987     88999999999999999999999999999999999999998876311100  00111123345


Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..|+|||.|++..+|+++|++.|++||.|..||+.++       +||+||.|.+.++|.+||..+| ++.+.|..++..|
T Consensus       163 ~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-------qGYaFVrF~tkEaAahAIv~mN-ntei~G~~VkCsW  234 (321)
T KOG0148|consen  163 DNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-------QGYAFVRFETKEAAAHAIVQMN-NTEIGGQLVRCSW  234 (321)
T ss_pred             CCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-------cceEEEEecchhhHHHHHHHhc-CceeCceEEEEec
Confidence            6899999999999999999999999999999999998       6999999999999999999997 6999999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      .++...
T Consensus       235 GKe~~~  240 (321)
T KOG0148|consen  235 GKEGDD  240 (321)
T ss_pred             cccCCC
Confidence            986554

>KOG4211|consensus

Probab=99.97  E-value=1.5e-30  Score=266.06  Aligned_cols=369  Identities=17%  Similarity=0.270  Sum_probs=250.5

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      .--|.+|+     |||+||++||.+||+.++ |+++.+.+. +|+.+|.|||.|++.||+++|+++ |+..|..|+|+|+
T Consensus        10 ~~~vr~rG-----LPwsat~~ei~~Ff~~~~-I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf   81 (510)
T KOG4211|consen   10 AFEVRLRG-----LPWSATEKEILDFFSNCG-IENLEIPRR-NGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVF   81 (510)
T ss_pred             ceEEEecC-----CCccccHHHHHHHHhcCc-eeEEEEecc-CCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEE
Confidence            34588888     999999999999999995 789666553 799999999999999999999999 9999999999999


Q ss_pred             EccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCCCc
Q psy3345          92 KCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGEE  171 (787)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (787)
                      .+..     .+..|                                               +|.+...            
T Consensus        82 ~~~~-----~e~d~-----------------------------------------------~~~~~g~------------   97 (510)
T KOG4211|consen   82 TAGG-----AEADW-----------------------------------------------VMRPGGP------------   97 (510)
T ss_pred             ccCC-----ccccc-----------------------------------------------cccCCCC------------
Confidence            8875     11111                                               1111100            


Q ss_pred             cccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCCCCc
Q psy3345         172 KEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA  251 (787)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v  251 (787)
                                                                     .......+|.|++||++||++||.+||+++.++
T Consensus        98 -----------------------------------------------~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv  130 (510)
T KOG4211|consen   98 -----------------------------------------------NSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIV  130 (510)
T ss_pred             -----------------------------------------------CCCCCCceEEecCCCccCcHHHHHHHhcCCccc
Confidence                                                           011356799999999999999999999999887


Q ss_pred             c--eeec------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecccCCcccc----------CCCcCCCC--ch-
Q psy3345         252 S--VRTT------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKY----------SGAADDNN--NA-  310 (787)
Q Consensus       252 ~--i~i~------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~~~~~~~~----------~~~~~~~~--~~-  310 (787)
                      .  |.++      ++|.|||.|.+.+.|+.||.+|...|+.|+|+|++.........          +.+.+...  .. 
T Consensus       131 ~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~  210 (510)
T KOG4211|consen  131 PDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGG  210 (510)
T ss_pred             ccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccc
Confidence            3  4444      67999999999999999999999999999999986221111100          01111100  00 


Q ss_pred             ---------------------------------------hhhhhhhccccc-----ccchhhh-hcccCCCCeEEEcCCC
Q psy3345         311 ---------------------------------------SMENIKAKHWKS-----QEDSVQF-AEDIAESGRIFVRNLS  345 (787)
Q Consensus       311 ---------------------------------------~~~~~~~~~~~~-----~~~~~~~-~~~~~~~~~l~V~nLp  345 (787)
                                                             +........+..     ....... ........+++.++||
T Consensus       211 ~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlp  290 (510)
T KOG4211|consen  211 YDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLP  290 (510)
T ss_pred             cccccccCCCccccccccccCCccccccCccccccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCC
Confidence                                                   000000000000     0000000 0111223789999999


Q ss_pred             CCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCC--
Q psy3345         346 YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVD--  423 (787)
Q Consensus       346 ~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~--  423 (787)
                      +..++.+|..+|+..-+ ..|+|... .+|+.+|.|+|+|.+.++|..|+. .++..++.+.+.+.............  
T Consensus       291 y~a~~~di~nfFspl~p-~~v~i~ig-~dGr~TGEAdveF~t~edav~Ams-kd~anm~hrYVElFln~~~ga~g~~~~s  367 (510)
T KOG4211|consen  291 YDATENDIANFFSPLNP-YRVHIEIG-PDGRATGEADVEFATGEDAVGAMG-KDGANMGHRYVELFLNGAPGASGGGGPS  367 (510)
T ss_pred             ccCCCcchhhhcCCCCc-eeEEEEeC-CCCccCCcceeecccchhhHhhhc-cCCcccCcceeeecccCCcccccCccCC
Confidence            99999999999998744 47777666 469999999999999999999996 68889999999886543221100000  


Q ss_pred             --------------C---Cccccccc-----------cccchhh-------------hhhhcCCCCEEEEeCCCCCCCHH
Q psy3345         424 --------------G---KVHCCISE-----------RKLDAFN-------------QVVEARSKRIILVKNLPYRTLPT  462 (787)
Q Consensus       424 --------------~---~~~~a~~~-----------~~~~~~~-------------~~~~~~~~~~i~v~nlp~~~t~~  462 (787)
                                    +   +.+...+.           ...+..+             ..........|-.+++|+..++.
T Consensus       368 ~~~g~~~~~~~~~~Gg~a~g~~~gG~~g~~~~~~~~G~~~~~~~~~~~~Gy~g~~~~~~~~~~e~~~~~~rgap~~a~ea  447 (510)
T KOG4211|consen  368 GPGGVGSSGDRNGGGGYASGSYGGGGNGGGGRGSPYGRPSDGYSSPGGGGYSGPRGYGRGPQNEHFVIRMRGAPFRASEA  447 (510)
T ss_pred             CCCCccccccccCCCCccccccccCCCCCccccCCCCCCcccccCCCCCCCcCcccCCCCccccccccCcCCCCcccccc
Confidence                          0   00000000           0000000             00122235678889999999999


Q ss_pred             HHHHhhccCCCee-EEEecC---CCcEEEEEeCCHHHHHHHHHH
Q psy3345         463 DLKALFEPFGDLG-RVLVPP---YGITGLVEFLQKNQAKAAFNS  502 (787)
Q Consensus       463 ~l~~~F~~~G~v~-~v~i~~---~~~~a~V~F~~~~~A~~A~~~  502 (787)
                      ++.++|.++++-. .+..+.   ..+.|-|-|.+.++++.|+.+
T Consensus       448 dv~d~~~~~~~a~~~~~yd~~~~~~~~a~~~~~~~~~~q~a~~~  491 (510)
T KOG4211|consen  448 DVYDFFHPIRPAQVELLYDHQFQRSGDARVIFYNRKDYQDALMK  491 (510)
T ss_pred             chhhcccccCcccccccccccccccCceeEEEechhhhHHHHHh
Confidence            9999999988642 222222   245799999999999999874

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.97  E-value=8.1e-30  Score=280.13  Aligned_cols=175  Identities=24%  Similarity=0.381  Sum_probs=149.2

Q ss_pred             ccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEe
Q psy3345         332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLI  411 (787)
Q Consensus       332 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~  411 (787)
                      .....++|||+|||+++++++|+++|+.||+|.+|.|+.++.+|+++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus       103 a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~  182 (612)
T TIGR01645       103 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  182 (612)
T ss_pred             hhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeec
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC------CCcE
Q psy3345         412 PGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGIT  485 (787)
Q Consensus       412 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~------~~~~  485 (787)
                      +.........       ..     +.  ........++|||+|||.++++++|+++|+.||.|.++.+.+      .+|+
T Consensus       183 rp~~~p~a~~-------~~-----~~--~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGf  248 (612)
T TIGR01645       183 RPSNMPQAQP-------II-----DM--VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGY  248 (612)
T ss_pred             cccccccccc-------cc-----cc--ccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCe
Confidence            6442210000       00     00  001122457899999999999999999999999999998865      3579


Q ss_pred             EEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecC
Q psy3345         486 GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  520 (787)
Q Consensus       486 a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  520 (787)
                      |||+|.+.++|.+|+..||+..++|+.|.|.++..
T Consensus       249 GFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       249 GFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             EEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            99999999999999999999999999999999853

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0144|consensus

Probab=99.97  E-value=8e-31  Score=262.22  Aligned_cols=269  Identities=24%  Similarity=0.411  Sum_probs=221.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCc-eeCC--eEEEE
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGT-VFLG--RMLHL  410 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~-~~~g--~~l~v  410 (787)
                      .+.-++||+-+|..++|.||+.+|++||.|.+|.|++|+.++.++|||||.|.+.++|.+|+.+||+. .|-|  .+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            34558999999999999999999999999999999999999999999999999999999999999864 2222  33333


Q ss_pred             eeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEe
Q psy3345         411 IPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEF  490 (787)
Q Consensus       411 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F  490 (787)
                      .++..                                                                           
T Consensus       112 k~Ad~---------------------------------------------------------------------------  116 (510)
T KOG0144|consen  112 KYADG---------------------------------------------------------------------------  116 (510)
T ss_pred             cccch---------------------------------------------------------------------------
Confidence            33221                                                                           


Q ss_pred             CCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccc
Q psy3345         491 LQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVE  570 (787)
Q Consensus       491 ~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  570 (787)
                                                    +                                                 
T Consensus       117 ------------------------------E-------------------------------------------------  117 (510)
T KOG0144|consen  117 ------------------------------E-------------------------------------------------  117 (510)
T ss_pred             ------------------------------h-------------------------------------------------
Confidence                                          1                                                 


Q ss_pred             cccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCC
Q psy3345         571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNS  650 (787)
Q Consensus       571 ~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~  650 (787)
                         .+.....+.|||+-|+..+|+.+++++|++||.|++|.|+++.+      +.|+|||||.|.+.+.|..|++.|||.
T Consensus       118 ---~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~------~~sRGcaFV~fstke~A~~Aika~ng~  188 (510)
T KOG0144|consen  118 ---RERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD------GLSRGCAFVKFSTKEMAVAAIKALNGT  188 (510)
T ss_pred             ---hhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc------ccccceeEEEEehHHHHHHHHHhhccc
Confidence               00011246799999999999999999999999999999999987      889999999999999999999999995


Q ss_pred             -ccCC--eEEEEEecCccccch----------------------------------------------------------
Q psy3345         651 -SLDE--HQIELKRSNRNLESE----------------------------------------------------------  669 (787)
Q Consensus       651 -~l~g--~~l~v~~~~~~~~~~----------------------------------------------------------  669 (787)
                       .+.|  .+|.|+|++....-.                                                          
T Consensus       189 ~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~  268 (510)
T KOG0144|consen  189 QTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGP  268 (510)
T ss_pred             eeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCC
Confidence             5666  489999997431110                                                          


Q ss_pred             --------------------------hh------hh----------------h-------------h-------------
Q psy3345         670 --------------------------AT------TV----------------K-------------R-------------  675 (787)
Q Consensus       670 --------------------------~~------~~----------------~-------------~-------------  675 (787)
                                                ..      .+                .             +             
T Consensus       269 l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~  348 (510)
T KOG0144|consen  269 LNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLA  348 (510)
T ss_pred             cchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccc
Confidence                                      00      00                0             0             


Q ss_pred             ------------------------------------------------------------------ccccccCCCCCEEE
Q psy3345         676 ------------------------------------------------------------------KSSNVAKQTGSKIL  689 (787)
Q Consensus       676 ------------------------------------------------------------------~~~~~~~~~~~~l~  689 (787)
                                                                                        .........+.+||
T Consensus       349 ~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlf  428 (510)
T KOG0144|consen  349 GGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLF  428 (510)
T ss_pred             cccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCcccee
Confidence                                                                              00011134689999


Q ss_pred             EecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccc
Q psy3345         690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEA  767 (787)
Q Consensus       690 V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~  767 (787)
                      |.+||-+.-+.||...|..||.|.+.++..++ -+|-+++|+||.|++..+|.+||..|| |.++++++|+|.....+
T Consensus       429 iyhlPqefgdq~l~~~f~pfG~Vlsakvfidk-~tnlskcfgfvSyen~~sa~~aI~amn-gfQig~KrlkVQlk~~~  504 (510)
T KOG0144|consen  429 IYHLPQEFGDQDLIATFQPFGGVLSAKVFIDK-VTNLSKCFGFVSYENAQSAQNAISAMN-GFQIGSKRLKVQLKRDR  504 (510)
T ss_pred             eeeCchhhhhHHHHHHhccccceeEEEEEEec-ccCHhhhcCcccccchhhhHHHHHHhc-chhhccccceEEeeecc
Confidence            99999999999999999999999999998886 689999999999999999999999997 79999999999987643

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.96  E-value=1.2e-28  Score=258.69  Aligned_cols=173  Identities=23%  Similarity=0.404  Sum_probs=155.5

Q ss_pred             CCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCe
Q psy3345         576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH  655 (787)
Q Consensus       576 ~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~  655 (787)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+|+++..     ++.++|||||+|.+.++|.+|+..|||..+.++
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~-----tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr  177 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYK-----TGYSFGYAFVDFGSEADSQRAIKNLNGITVRNK  177 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC-----CCccCcEEEEEEccHHHHHHHHHHcCCCccCCc
Confidence            445678999999999999999999999999999999998876     678999999999999999999999999999999


Q ss_pred             EEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEe
Q psy3345         656 QIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF  735 (787)
Q Consensus       656 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F  735 (787)
                      +|+|.++.....              ....++|||.|||..+|+++|+++|++||.|..++|+++. .+|+++|||||+|
T Consensus       178 ~i~V~~a~p~~~--------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~-~tg~~kG~aFV~F  242 (346)
T TIGR01659       178 RLKVSYARPGGE--------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK-LTGTPRGVAFVRF  242 (346)
T ss_pred             eeeeeccccccc--------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecC-CCCccceEEEEEE
Confidence            999998764322              1235789999999999999999999999999999999885 6899999999999


Q ss_pred             cCHHHHHHHHHHhcCCeeecC--ceEEEEEcccccc
Q psy3345         736 ITKNEAKRAMKALCQSTHLYG--RRLVLEWAEEADN  769 (787)
Q Consensus       736 ~~~~~A~~Al~~l~~~~~~~G--r~l~v~~A~~~~~  769 (787)
                      .+.++|.+||+.|| +..+.|  ++|.|.||++...
T Consensus       243 ~~~e~A~~Ai~~ln-g~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       243 NKREEAQEAISALN-NVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             CCHHHHHHHHHHhC-CCccCCCceeEEEEECCcccc
Confidence            99999999999997 687766  7999999986543

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0144|consensus

Probab=99.96  E-value=5.5e-29  Score=249.08  Aligned_cols=159  Identities=22%  Similarity=0.367  Sum_probs=134.2

Q ss_pred             ccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-------ccceEEEeecChHhHHHHHh-cC-CcccCCe--eEEEe
Q psy3345         223 QYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-------FLGMAYIGFKDEKNCNKALN-KN-KSFWKGK--QLNIY  290 (787)
Q Consensus       223 ~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-------~~g~afV~F~~~~~A~~Al~-~~-~~~l~g~--~i~v~  290 (787)
                      +.-.+||+-||.+++|.||+++|..||.| +|.|+       ++|||||.|.+.++|.+|+. +| .+.|.|.  +|.|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            34569999999999999999999999998 78777       67999999999999999998 54 5667664  55552


Q ss_pred             ecccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEec
Q psy3345         291 KYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPI  370 (787)
Q Consensus       291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~  370 (787)
                      + +                                 +.+.+...+.++|||+-|+..+||.+|+++|++||.|.+|.|++
T Consensus       113 ~-A---------------------------------d~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilr  158 (510)
T KOG0144|consen  113 Y-A---------------------------------DGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILR  158 (510)
T ss_pred             c-c---------------------------------chhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhhee
Confidence            1 0                                 01112334567899999999999999999999999999999999


Q ss_pred             CCCCCCcceEEEEEEcCHHHHHHHHHHhCCc-eeCC--eEEEEeeCCCC
Q psy3345         371 DKETDKTKGFALVTFLMPEHATQAYQHLDGT-VFLG--RMLHLIPGKPK  416 (787)
Q Consensus       371 ~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~-~~~g--~~l~v~~~~~~  416 (787)
                      +. .+.++|||||.|.+.+.|..|++.|||. .+.|  .+|.|.|+.++
T Consensus       159 d~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtq  206 (510)
T KOG0144|consen  159 DP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQ  206 (510)
T ss_pred             cc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccC
Confidence            85 5899999999999999999999999996 4544  79999999876

>KOG1190|consensus

Probab=99.95  E-value=1.1e-26  Score=231.04  Aligned_cols=410  Identities=17%  Similarity=0.198  Sum_probs=277.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCc--eeCCeEEEEe
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGT--VFLGRMLHLI  411 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~--~~~g~~l~v~  411 (787)
                      .+++.|++||||.+++|++|..++.+||.|..+.+.+.+      ..||++|.+.+.|..-+..+...  .+.|++|.|.
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGk------nQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq   99 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGK------NQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQ   99 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccceeeeeeeccc------hhhhhhhcchhhhhheeecccccCccccCcceeeh
Confidence            367789999999999999999999999999999886543      27999999999998855433222  5688999988


Q ss_pred             eCCCCCCCCCCC-----C-Cc---cccccccccc--h--hh--hhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeE
Q psy3345         412 PGKPKENEGNVD-----G-KV---HCCISERKLD--A--FN--QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR  476 (787)
Q Consensus       412 ~~~~~~~~~~~~-----~-~~---~~a~~~~~~~--~--~~--~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~  476 (787)
                      ++.-.+......     + .+   -.+..+..+.  .  ..  .......--.++|.|+-+.++.+-|..+|++||.|.+
T Consensus       100 ~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlK  179 (492)
T KOG1190|consen  100 YSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLK  179 (492)
T ss_pred             hhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEE
Confidence            865432111100     0 00   0000010000  0  00  1111223445778999999999999999999999998


Q ss_pred             EEecC-CCc-EEEEEeCCHHHHHHHHHHhcCCeeCC--eeEEEEEecCccccccccccccccccccccccccchhhhhcc
Q psy3345         477 VLVPP-YGI-TGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKEN  552 (787)
Q Consensus       477 v~i~~-~~~-~a~V~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  552 (787)
                      |.-.. +.+ .|+|+|.+++.|..|...|+|+.++.  +.|+++|..-..........+.+............++.-...
T Consensus       180 IiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~  259 (492)
T KOG1190|consen  180 IITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQL  259 (492)
T ss_pred             EEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchh
Confidence            77554 555 59999999999999999999999873  688899887766666666555554221111111111100000


Q ss_pred             cccccc--------cCCCcccccc-cccccccCCC-CCCeEEecCCCCC-CCHHHHHHHHhhcCCeEEEEEeecCCCCCC
Q psy3345         553 TAEEDN--------QQGVPEVEEN-VEEDEEREPE-PDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTVARKKDPKSP  621 (787)
Q Consensus       553 ~~~~~~--------~~~~~~~~~~-~~~~~~~~~~-~~~~l~V~NLp~~-~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~  621 (787)
                      ......        ....+..... .......... ....|.|.||... +|.+-|..+|..||.|..|+|+.++.    
T Consensus       260 ~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk----  335 (492)
T KOG1190|consen  260 MAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK----  335 (492)
T ss_pred             hhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC----
Confidence            000000        0000000000 0000011111 2578899999776 89999999999999999999998653    


Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccch---------------hhhhhhcccc------c
Q psy3345         622 GQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESE---------------ATTVKRKSSN------V  680 (787)
Q Consensus       622 ~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~---------------~~~~~~~~~~------~  680 (787)
                            --|.|+|.+..+|+-|+..|+|..|.|+.|+|.+++...-..               .....+.+.+      .
T Consensus       336 ------d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~n  409 (492)
T KOG1190|consen  336 ------DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQN  409 (492)
T ss_pred             ------cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccc
Confidence                  469999999999999999999999999999999997532210               0111111111      1


Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC-ceE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG-RRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G-r~l  759 (787)
                      ...|+.+|++.|+|..+++++|+..|..-|...+...  .   -+..+.+|.+.+.+.++|..|+..+.+ ..+.+ ..|
T Consensus       410 i~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafk--f---f~kd~kmal~q~~sveeA~~ali~~hn-h~lgen~hl  483 (492)
T KOG1190|consen  410 IFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFK--F---FQKDRKMALPQLESVEEAIQALIDLHN-HYLGENHHL  483 (492)
T ss_pred             cCCchhheeeccCCcccchhHHHHhhhcCCceEEeee--e---cCCCcceeecccCChhHhhhhcccccc-ccCCCCceE
Confidence            1347789999999999999999999998887644332  1   133567999999999999999999953 66665 599


Q ss_pred             EEEEcc
Q psy3345         760 VLEWAE  765 (787)
Q Consensus       760 ~v~~A~  765 (787)
                      +|+|.+
T Consensus       484 RvSFSk  489 (492)
T KOG1190|consen  484 RVSFSK  489 (492)
T ss_pred             EEEeec
Confidence            999986

>KOG1190|consensus

Probab=99.95  E-value=2.4e-26  Score=228.61  Aligned_cols=409  Identities=19%  Similarity=0.199  Sum_probs=266.1

Q ss_pred             CccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-ccceEEEeecChHhHHHHHhc---CCcccCCeeEEEeecccCC
Q psy3345         222 RQYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-FLGMAYIGFKDEKNCNKALNK---NKSFWKGKQLNIYKYSKDN  296 (787)
Q Consensus       222 ~~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-~~g~afV~F~~~~~A~~Al~~---~~~~l~g~~i~v~~~~~~~  296 (787)
                      ..+++|++||||.+++|.||.+++.+||.+ .+.++ .+..||++|.++++|...+..   -.-.|.|++|.|+.   .+
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~---sn  102 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQY---SN  102 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccceeeeeeeccchhhhhhhcchhhhhheeecccccCccccCcceeehh---hh
Confidence            467899999999999999999999999998 55554 667999999999999886662   24567888888852   11


Q ss_pred             cccc--C-CCcCCCCchhhhh-----hhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q psy3345         297 SAKY--S-GAADDNNNASMEN-----IKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVIL  368 (787)
Q Consensus       297 ~~~~--~-~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i  368 (787)
                      ....  . .+...........     ....+.+..............--+++|.|+-+.++-+-|..+|++||.|..|.-
T Consensus       103 ~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiT  182 (492)
T KOG1190|consen  103 HSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIIT  182 (492)
T ss_pred             HHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEE
Confidence            1110  0 0000000000000     000000000000001111223347889999999999999999999999999765


Q ss_pred             ecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeE--EEEeeCCCC--------CCCCCCC------C--------
Q psy3345         369 PIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRM--LHLIPGKPK--------ENEGNVD------G--------  424 (787)
Q Consensus       369 ~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~--l~v~~~~~~--------~~~~~~~------~--------  424 (787)
                      ...    ...-.|.|+|.+.+.|+.|...|+|+.|..-+  |+|.++.-.        +++.+..      +        
T Consensus       183 F~K----nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~  258 (492)
T KOG1190|consen  183 FTK----NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQ  258 (492)
T ss_pred             Eec----ccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccch
Confidence            432    12225999999999999999999999886644  444443221        0111000      0        


Q ss_pred             -------Cc------cccccc---cccchhhhhhhcCCCCEEEEeCCCC-CCCHHHHHHhhccCCCeeEEEecCCC-cEE
Q psy3345         425 -------KV------HCCISE---RKLDAFNQVVEARSKRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYG-ITG  486 (787)
Q Consensus       425 -------~~------~~a~~~---~~~~~~~~~~~~~~~~~i~v~nlp~-~~t~~~l~~~F~~~G~v~~v~i~~~~-~~a  486 (787)
                             +.      ..++..   ..............+..|.|.||.. .+|.+-|..+|..||.|.+|.|..++ ..|
T Consensus       259 ~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~A  338 (492)
T KOG1190|consen  259 LMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNA  338 (492)
T ss_pred             hhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcce
Confidence                   00      000000   0000000000111267889999865 58999999999999999999998755 489


Q ss_pred             EEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccc
Q psy3345         487 LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVE  566 (787)
Q Consensus       487 ~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  566 (787)
                      +|+|.+..+|..|+..|+|..++|++|+|.+..-....-+....                  +......+....+.+...
T Consensus       339 LIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq------------------~d~glT~dy~~spLhrfk  400 (492)
T KOG1190|consen  339 LIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQ------------------EDQGLTKDYGNSPLHRFK  400 (492)
T ss_pred             eeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCC------------------ccccccccCCCCchhhcc
Confidence            99999999999999999999999999999988543111111000                  001111111222222222


Q ss_pred             cccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHH
Q psy3345         567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKV  646 (787)
Q Consensus       567 ~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~  646 (787)
                      ....+.......+..+|.+.|||.++++++++++|..-|...+.....         +..+-++++.+.+.++|..|+..
T Consensus       401 kpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff---------~kd~kmal~q~~sveeA~~ali~  471 (492)
T KOG1190|consen  401 KPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF---------QKDRKMALPQLESVEEAIQALID  471 (492)
T ss_pred             CcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec---------CCCcceeecccCChhHhhhhccc
Confidence            222222233446678999999999999999999999998765554443         23456999999999999999999


Q ss_pred             hCCCccCC-eEEEEEecCc
Q psy3345         647 LQNSSLDE-HQIELKRSNR  664 (787)
Q Consensus       647 lng~~l~g-~~l~v~~~~~  664 (787)
                      ++++.+++ +.|+|+|++.
T Consensus       472 ~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  472 LHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cccccCCCCceEEEEeecc
Confidence            99999875 6999999864

>KOG4211|consensus

Probab=99.94  E-value=1.2e-25  Score=230.26  Aligned_cols=418  Identities=17%  Similarity=0.226  Sum_probs=261.9

Q ss_pred             CCccceEEEeCCCCCCCHHhHHHhhcCCCCcceeec-----ccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecccC
Q psy3345         221 KRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTT-----FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKD  295 (787)
Q Consensus       221 ~~~~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~-----~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~~~  295 (787)
                      ......|.+++||+++|++||++||+.+++.++.+.     ++|.|||+|.+++++++||+++...|..|+|+|++....
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCc
Confidence            346789999999999999999999999999886666     668999999999999999999999999999999842221


Q ss_pred             CccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEecCCCC
Q psy3345         296 NSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE-VILPIDKET  374 (787)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~~~~  374 (787)
                      ..                     .|......   .........|.+++||+.+|++||.+||+..-.+.. |.++.+. .
T Consensus        87 e~---------------------d~~~~~~g---~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-r  141 (510)
T KOG4211|consen   87 EA---------------------DWVMRPGG---PNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-R  141 (510)
T ss_pred             cc---------------------cccccCCC---CCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-C
Confidence            11                     12100000   011134568999999999999999999998744444 4455554 5


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeC
Q psy3345         375 DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKN  454 (787)
Q Consensus       375 ~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~n  454 (787)
                      ++++|.|||+|++.+.|++|+. .|...|..|.|.|..+...+........                       .+.+.-
T Consensus       142 gR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss~~e~~~~~~~~-----------------------~~~~~r  197 (510)
T KOG4211|consen  142 GRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSSRAEVKRAAGPG-----------------------DGRVGR  197 (510)
T ss_pred             CCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhHHHHHHhhcccc-----------------------ccccCC
Confidence            8899999999999999999997 5778999999999887654221111000                       000000


Q ss_pred             -CCCCCCHHHHHHhhccCCCeeE-------EEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCcccccc
Q psy3345         455 -LPYRTLPTDLKALFEPFGDLGR-------VLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEA  526 (787)
Q Consensus       455 -lp~~~t~~~l~~~F~~~G~v~~-------v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~  526 (787)
                       =|+..- .-.+-... |+.-..       -.....+..+|+.+....+-..     -+....++.+..  ....     
T Consensus       198 pGpy~~~-~a~Rg~~d-~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~-----~gs~~~~~~~~~--~~~~-----  263 (510)
T KOG4211|consen  198 PGPYDRP-GAPRGGYD-YGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGN-----FGSYGGGRDPNY--PVSS-----  263 (510)
T ss_pred             CCccccc-cCCccccc-cccccCCCccccccccccCCccccccCcccccccc-----cccccccccccc--CCCC-----
Confidence             000000 00000000 000000       0000111122222221110000     000000000000  0000     


Q ss_pred             ccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCC
Q psy3345         527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP  606 (787)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~  606 (787)
                                     .+                    . ..............+..+..++||+..+..++.++|+..-.
T Consensus       264 ---------------g~--------------------~-~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p  307 (510)
T KOG4211|consen  264 ---------------GP--------------------H-RQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNP  307 (510)
T ss_pred             ---------------Cc--------------------c-cCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCc
Confidence                           00                    0 00000000112223378999999999999999999997665


Q ss_pred             eEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccch-----------------
Q psy3345         607 IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESE-----------------  669 (787)
Q Consensus       607 v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~-----------------  669 (787)
                      + .|.|-..++      ++.+|-|+|+|.|.++|..|+. -++..+..+-+.+..........                 
T Consensus       308 ~-~v~i~ig~d------Gr~TGEAdveF~t~edav~Ams-kd~anm~hrYVElFln~~~ga~g~~~~s~~~g~~~~~~~~  379 (510)
T KOG4211|consen  308 Y-RVHIEIGPD------GRATGEADVEFATGEDAVGAMG-KDGANMGHRYVELFLNGAPGASGGGGPSGPGGVGSSGDRN  379 (510)
T ss_pred             e-eEEEEeCCC------CccCCcceeecccchhhHhhhc-cCCcccCcceeeecccCCcccccCccCCCCCCcccccccc
Confidence            5 777777665      7899999999999999999998 45677777666664432110000                 


Q ss_pred             --------h----------------hhhhh-------------ccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCe
Q psy3345         670 --------A----------------TTVKR-------------KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGEL  712 (787)
Q Consensus       670 --------~----------------~~~~~-------------~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I  712 (787)
                              .                .....             .-...+......|..+++|...++.|+.++|.+++ -
T Consensus       380 ~~Gg~a~g~~~gG~~g~~~~~~~~G~~~~~~~~~~~~Gy~g~~~~~~~~~~e~~~~~~rgap~~a~eadv~d~~~~~~-~  458 (510)
T KOG4211|consen  380 GGGGYASGSYGGGGNGGGGRGSPYGRPSDGYSSPGGGGYSGPRGYGRGPQNEHFVIRMRGAPFRASEADVYDFFHPIR-P  458 (510)
T ss_pred             CCCCccccccccCCCCCccccCCCCCCcccccCCCCCCCcCcccCCCCccccccccCcCCCCccccccchhhcccccC-c
Confidence                    0                00000             00001122456778899999999999999999988 4


Q ss_pred             eEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHh
Q psy3345         713 KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL  748 (787)
Q Consensus       713 ~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l  748 (787)
                      -.|.+..+  ...++.|-|-|.|.+.++++.||..-
T Consensus       459 a~~~~~yd--~~~~~~~~a~~~~~~~~~~q~a~~~~  492 (510)
T KOG4211|consen  459 AQVELLYD--HQFQRSGDARVIFYNRKDYQDALMKD  492 (510)
T ss_pred             cccccccc--ccccccCceeEEEechhhhHHHHHhh
Confidence            56888888  46777889999999999999999873

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.94  E-value=1.5e-25  Score=235.32  Aligned_cols=164  Identities=22%  Similarity=0.327  Sum_probs=147.6

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ....++|||+|||+++|+++|+++|+.||+|.+|+|+.+..+++++|||||+|.+.++|.+|++.|++..+.++.|.|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC------CcEE
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITG  486 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a  486 (787)
                      +.+..                         .....++|+|.|||..+++++|+++|++||.|..+.|.++      +++|
T Consensus       184 a~p~~-------------------------~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~a  238 (346)
T TIGR01659       184 ARPGG-------------------------ESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVA  238 (346)
T ss_pred             ccccc-------------------------cccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEE
Confidence            76431                         1123568999999999999999999999999998888764      3699


Q ss_pred             EEEeCCHHHHHHHHHHhcCCeeCC--eeEEEEEecCc
Q psy3345         487 LVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEG  521 (787)
Q Consensus       487 ~V~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~~~~~  521 (787)
                      ||+|.+.++|.+|++.|++..+.+  ++|.|.|+...
T Consensus       239 FV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       239 FVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             EEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            999999999999999999998875  78999998654

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG4212|consensus

Probab=99.93  E-value=9.1e-25  Score=218.55  Aligned_cols=242  Identities=19%  Similarity=0.237  Sum_probs=192.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFE-KYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ..+.+||.|+||++...+|+++|. +.|.|..|.+..| ..|+++|||.|+|+++|.+++|++.||...+.||+|.|+-.
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            345699999999999999999996 6799999999998 46999999999999999999999999999999999999765


Q ss_pred             CCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC-----CCcEEEE
Q psy3345         414 KPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLV  488 (787)
Q Consensus       414 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~-----~~~~a~V  488 (787)
                      ...+...                   .....+.....++.++...+-..-|...|+--|.+.+-.+.+     +++..++
T Consensus       122 ~d~q~~~-------------------~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~  182 (608)
T KOG4212|consen  122 HDEQRDQ-------------------YGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTN  182 (608)
T ss_pred             Cchhhhh-------------------hhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCcc
Confidence            4321110                   112344567789999999998888888888777655444433     3346789


Q ss_pred             EeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccc
Q psy3345         489 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEEN  568 (787)
Q Consensus       489 ~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  568 (787)
                      .|.+.-.+..++.-++.....-+++.+ +.|+                                                
T Consensus       183 t~~~~~~~~~~~~lfgl~~~Flr~~h~-f~pP------------------------------------------------  213 (608)
T KOG4212|consen  183 TMSNDYNNSSNYNLFGLSASFLRSLHI-FSPP------------------------------------------------  213 (608)
T ss_pred             ccccccccchhhhcccchhhhhhhccC-CCCC------------------------------------------------
Confidence            998888888777755555444454443 2222                                                


Q ss_pred             cccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy3345         569 VEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQ  648 (787)
Q Consensus       569 ~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~ln  648 (787)
                                ....+||.||.+.+....|.+.|.-.|.|.++.+-.++.      +.++||+.++|..+-+|..|+..++
T Consensus       214 ----------l~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe------G~s~G~~vi~y~hpveavqaIsml~  277 (608)
T KOG4212|consen  214 ----------LHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE------GNSRGFAVIEYDHPVEAVQAISMLD  277 (608)
T ss_pred             ----------ccceeeeeccccccchHHHHHHhccceeeeeeceeeccc------cccCCeeEEEecchHHHHHHHHhhc
Confidence                      234689999999999999999999999999999988876      6889999999999999999999998


Q ss_pred             CCccCCeEEEEEe
Q psy3345         649 NSSLDEHQIELKR  661 (787)
Q Consensus       649 g~~l~g~~l~v~~  661 (787)
                      +.-+..++..+.+
T Consensus       278 ~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  278 RQGLFDRRMTVRL  290 (608)
T ss_pred             cCCCccccceeec
Confidence            7666666555544

>KOG0147|consensus

Probab=99.93  E-value=3.6e-26  Score=237.32  Aligned_cols=290  Identities=22%  Similarity=0.276  Sum_probs=222.5

Q ss_pred             cCCCccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEe
Q psy3345         219 VHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIY  290 (787)
Q Consensus       219 ~~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~  290 (787)
                      ...|..++|++.-|+...++.||.+||+..|.| +|+++       ++|.|||+|.+.+....|+.+.|..+.|.+|.|.
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQ  253 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEec
Confidence            456788999999999999999999999999998 89988       6799999999999999999999999999999995


Q ss_pred             ec-ccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe
Q psy3345         291 KY-SKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP  369 (787)
Q Consensus       291 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~  369 (787)
                      .- ++++.. +               ....|-      +...-..+..+|||+||.+++|++.|+.+|++||.|..|.++
T Consensus       254 ~sEaeknr~-a---------------~~s~a~------~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~  311 (549)
T KOG0147|consen  254 LSEAEKNRA-A---------------NASPAL------QGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLT  311 (549)
T ss_pred             ccHHHHHHH-H---------------hccccc------cccccccchhhhhhcccccCchHHHHhhhccCcccceeeeec
Confidence            20 000000 0               000110      000112233349999999999999999999999999999999


Q ss_pred             cCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC-CCCCC------CC-----CCccccccc-----
Q psy3345         370 IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK-ENEGN------VD-----GKVHCCISE-----  432 (787)
Q Consensus       370 ~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~-~~~~~------~~-----~~~~~a~~~-----  432 (787)
                      ++..||.++||+||+|.+.++|++|+.+|||..+-|+.|+|...... .....      .+     +-.-.+.+.     
T Consensus       312 ~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~  391 (549)
T KOG0147|consen  312 KDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMA  391 (549)
T ss_pred             cccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHH
Confidence            99889999999999999999999999999999999999999876554 11100      00     000000000     


Q ss_pred             -----------------------cccch-------hhhhhhc-------CCCCEEEEeCCCCCCC----------HHHHH
Q psy3345         433 -----------------------RKLDA-------FNQVVEA-------RSKRIILVKNLPYRTL----------PTDLK  465 (787)
Q Consensus       433 -----------------------~~~~~-------~~~~~~~-------~~~~~i~v~nlp~~~t----------~~~l~  465 (787)
                                             .....       .......       .++.|++++|+-...|          .+|+.
T Consensus       392 kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~  471 (549)
T KOG0147|consen  392 KLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVI  471 (549)
T ss_pred             HHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHH
Confidence                                   00000       0001111       4567888899843322          36889


Q ss_pred             HhhccCCCeeEEEecCCC-cEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCcccccccccc
Q psy3345         466 ALFEPFGDLGRVLVPPYG-ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKS  530 (787)
Q Consensus       466 ~~F~~~G~v~~v~i~~~~-~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~  530 (787)
                      +.|.+||.|.+|.++++. |+.||.|.+.+.|..|+..|||++|.|+.|...|.+...|...++..
T Consensus       472 Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~~Y~~~FP~~  537 (549)
T KOG0147|consen  472 EECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLERYHSKFPDS  537 (549)
T ss_pred             HHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehhhhhhhCCCc
Confidence            999999999999999966 99999999999999999999999999999999999998887777654

>KOG0124|consensus

Probab=99.92  E-value=6.1e-24  Score=207.87  Aligned_cols=277  Identities=25%  Similarity=0.416  Sum_probs=215.5

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ..-.|+|||+.+.+.+.|+.|+..|.+||+|.+|.+-.|+-|++++|||||+|.-++.|+-|++.|||..++||.|+|..
T Consensus       110 LaiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  110 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             HHHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            34467999999999999999999999999999999999999999999999999999999999999999999999999853


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCC
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQ  492 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~  492 (787)
                      ..                                       |+|.                                   
T Consensus       190 Ps---------------------------------------NmpQ-----------------------------------  195 (544)
T KOG0124|consen  190 PS---------------------------------------NMPQ-----------------------------------  195 (544)
T ss_pred             CC---------------------------------------CCcc-----------------------------------
Confidence            22                                       1221                                   


Q ss_pred             HHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccc
Q psy3345         493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEED  572 (787)
Q Consensus       493 ~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  572 (787)
                         |+-.+..+.                                                                    
T Consensus       196 ---AQpiID~vq--------------------------------------------------------------------  204 (544)
T KOG0124|consen  196 ---AQPIIDMVQ--------------------------------------------------------------------  204 (544)
T ss_pred             ---cchHHHHHH--------------------------------------------------------------------
Confidence               111111000                                                                    


Q ss_pred             cccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy3345         573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL  652 (787)
Q Consensus       573 ~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l  652 (787)
                        .+...-.+|||..+.++.++++|+..|+.||.|.+|.+.+.+.     .+..+||||++|.+...-..|+..||-+.|
T Consensus       205 --eeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt-----~~~HkGyGfiEy~n~qs~~eAiasMNlFDL  277 (544)
T KOG0124|consen  205 --EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT-----GRGHKGYGFIEYNNLQSQSEAIASMNLFDL  277 (544)
T ss_pred             --HHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCC-----CCCccceeeEEeccccchHHHhhhcchhhc
Confidence              0001135799999999999999999999999999999998775     567999999999999999999999999999


Q ss_pred             CCeEEEEEecCccccc----------h-------------------------------------------------hh--
Q psy3345         653 DEHQIELKRSNRNLES----------E-------------------------------------------------AT--  671 (787)
Q Consensus       653 ~g~~l~v~~~~~~~~~----------~-------------------------------------------------~~--  671 (787)
                      +|.-|+|..+-.....          +                                                 ..  
T Consensus       278 GGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~  357 (544)
T KOG0124|consen  278 GGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVM  357 (544)
T ss_pred             ccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccch
Confidence            9999999876532111          0                                                 00  


Q ss_pred             --------------------------------------------------hhhhcc------------------------
Q psy3345         672 --------------------------------------------------TVKRKS------------------------  677 (787)
Q Consensus       672 --------------------------------------------------~~~~~~------------------------  677 (787)
                                                                        ..+.+.                        
T Consensus       358 a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvM  437 (544)
T KOG0124|consen  358 AAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVM  437 (544)
T ss_pred             hccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHH
Confidence                                                              000000                        


Q ss_pred             -ccccCCCCCEEEEecC--CccCc---HHHHHHHHHhcCCeeEEEeccccCCCCCC-----ceEEEEEecCHHHHHHHHH
Q psy3345         678 -SNVAKQTGSKILVRNI--PFQAK---QSEVEELFKAFGELKFVRLPKKMVGSGLH-----RGFGFVEFITKNEAKRAMK  746 (787)
Q Consensus       678 -~~~~~~~~~~l~V~nL--p~~~t---~~dL~~~F~~~G~I~~v~i~~~~~~~g~~-----~g~afV~F~~~~~A~~Al~  746 (787)
                       .......++.+.++|+  |.+++   +.+|++.|++||.|..|-|....  .+..     ----||+|+...++.+|.+
T Consensus       438 qkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nek--q~e~edaeiiVKIFVefS~~~e~~rak~  515 (544)
T KOG0124|consen  438 QKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEK--QGEEEDAEIIVKIFVEFSIASETHRAKQ  515 (544)
T ss_pred             HHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecc--cccccchhhhheeeeeechhhHHHHHHH
Confidence             0001336778888998  55555   45799999999999998886653  1211     1136999999999999999


Q ss_pred             HhcCCeeecCceEEEEEc
Q psy3345         747 ALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       747 ~l~~~~~~~Gr~l~v~~A  764 (787)
                      +|+ |++|.||+++.+..
T Consensus       516 ALd-GRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  516 ALD-GRFFGGRKVVAEVY  532 (544)
T ss_pred             hhc-cceecCceeehhhh
Confidence            997 79999999987654

>KOG1456|consensus

Probab=99.92  E-value=5.4e-22  Score=195.19  Aligned_cols=396  Identities=19%  Similarity=0.200  Sum_probs=271.6

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHH--HhCCceeCCeEEEE
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ--HLDGTVFLGRMLHL  410 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~--~l~~~~~~g~~l~v  410 (787)
                      ...+-.|+|++|-..++|.+|.+.++.||+|..+.++..+      ..|.|+|.+.+-|..++.  +-+...+.|+.-.+
T Consensus        28 ~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~------r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~  101 (494)
T KOG1456|consen   28 PNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK------RQALVEFEDIEGAKNCVNFAADNQIYIAGQQALF  101 (494)
T ss_pred             CCCCceEEEeccccccchhHHHHHHhcCCceEEEEecccc------ceeeeeeccccchhhheehhccCcccccCchhhc
Confidence            3456689999999999999999999999999988876543      379999999999999875  22334667777666


Q ss_pred             eeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEe--CCCCCCCHHHHHHhhccCCCeeEEEecC-CCcEEE
Q psy3345         411 IPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK--NLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGL  487 (787)
Q Consensus       411 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~--nlp~~~t~~~l~~~F~~~G~v~~v~i~~-~~~~a~  487 (787)
                      .++..+.....                  ......++.+|++.  |--+.+|.+-|..++...|.|.+|.|.+ ++-.|.
T Consensus       102 NyStsq~i~R~------------------g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAm  163 (494)
T KOG1456|consen  102 NYSTSQCIERP------------------GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAM  163 (494)
T ss_pred             ccchhhhhccC------------------CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeE
Confidence            66644311100                  01122334555544  5557899999999999999999999877 555899


Q ss_pred             EEeCCHHHHHHHHHHhcCCeeC-C-eeEEEEEecCcccccccccccccccccccc-------cc---ccch-------hh
Q psy3345         488 VEFLQKNQAKAAFNSLAYTKFK-E-VPLYLEWAPEGVFAEAKEKSKGKEKEKNEE-------EG---EEGE-------EE  548 (787)
Q Consensus       488 V~F~~~~~A~~A~~~l~~~~~~-g-~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~-------~~---~~~~-------~~  548 (787)
                      |+|.+.+.|++|...|||.-++ | ++|.|+|+.+.........+..........       ..   +..+       ..
T Consensus       164 VEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~ps  243 (494)
T KOG1456|consen  164 VEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPS  243 (494)
T ss_pred             EeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChh
Confidence            9999999999999999999888 3 789999997764332221111111000000       00   0000       00


Q ss_pred             hhcccccc----cccCCC---cc-----cccccccccccCCCCCCeEEecCCCCC-CCHHHHHHHHhhcCCeEEEEEeec
Q psy3345         549 KKENTAEE----DNQQGV---PE-----VEENVEEDEEREPEPDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTVARK  615 (787)
Q Consensus       549 ~~~~~~~~----~~~~~~---~~-----~~~~~~~~~~~~~~~~~~l~V~NLp~~-~t~~~L~~~F~~~G~v~~v~i~~~  615 (787)
                      ........    ....+.   ++     ..+...........+++.++|.+|... ++.+.|.++|..||.|..+++++.
T Consensus       244 s~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkT  323 (494)
T KOG1456|consen  244 SRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKT  323 (494)
T ss_pred             hcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeec
Confidence            00000000    000000   00     001011111244567899999999986 678999999999999999999986


Q ss_pred             CCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhh--------hh---------hhc--
Q psy3345         616 KDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEAT--------TV---------KRK--  676 (787)
Q Consensus       616 ~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~--------~~---------~~~--  676 (787)
                      +.          |.|.|++.+..+.++|+..||+..+-|.+|.|..++...-.+..        .+         .+.  
T Consensus       324 k~----------gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFss  393 (494)
T KOG1456|consen  324 KP----------GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSS  393 (494)
T ss_pred             cc----------ceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCC
Confidence            65          89999999999999999999999999999999998754322110        00         000  


Q ss_pred             ----cccccCCCCCEEEEecCCccCcHHHHHHHHHhcCC-eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCC
Q psy3345         677 ----SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS  751 (787)
Q Consensus       677 ----~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~-I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~  751 (787)
                          .......|++.|+..|.|..+||+.|.++|..-+. -++++|..-+  +.+ ...|.++|.+..+|..||..+|| 
T Consensus       394 p~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k--ser-SssGllEfe~~s~Aveal~~~NH-  469 (494)
T KOG1456|consen  394 PEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK--SER-SSSGLLEFENKSDAVEALMKLNH-  469 (494)
T ss_pred             hhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc--ccc-cccceeeeehHHHHHHHHHHhcc-
Confidence                01111347899999999999999999999986654 3567775553  232 33589999999999999999997 


Q ss_pred             eeecCc------eEEEEEccc
Q psy3345         752 THLYGR------RLVLEWAEE  766 (787)
Q Consensus       752 ~~~~Gr------~l~v~~A~~  766 (787)
                      ..+.|.      .|++.|+.+
T Consensus       470 ~pi~~p~gs~PfilKlcfsts  490 (494)
T KOG1456|consen  470 YPIEGPNGSFPFILKLCFSTS  490 (494)
T ss_pred             ccccCCCCCCCeeeeeeeccc
Confidence            777762      566666654

>KOG0124|consensus

Probab=99.92  E-value=3.4e-24  Score=209.66  Aligned_cols=277  Identities=16%  Similarity=0.248  Sum_probs=211.4

Q ss_pred             ceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-------ccceEEEeecChHhHHHHHh-cCCcccCCeeEEEeecccC
Q psy3345         225 HTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-------FLGMAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYSKD  295 (787)
Q Consensus       225 ~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-------~~g~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~~~  295 (787)
                      |+|||+.|.+...|+.|+..|.+||++ +|.+.       .+|+|||+|.-+|.|+-|+. +|+..|+||.|.|-  .+.
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg--rPs  191 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG--RPS  191 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc--CCC
Confidence            789999999999999999999999998 67665       67999999999999999999 99999999999994  333


Q ss_pred             CccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCC
Q psy3345         296 NSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD  375 (787)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~  375 (787)
                      +++...                      .-.+........-.+|||..+.++.+++||+.+|+.||+|..|.+-+++.++
T Consensus       192 NmpQAQ----------------------piID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~  249 (544)
T KOG0124|consen  192 NMPQAQ----------------------PIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGR  249 (544)
T ss_pred             CCcccc----------------------hHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCC
Confidence            333211                      1111112222334589999999999999999999999999999999998888


Q ss_pred             CcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCC-CC--CCCC-----------------------------
Q psy3345         376 KTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE-NE--GNVD-----------------------------  423 (787)
Q Consensus       376 ~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~-~~--~~~~-----------------------------  423 (787)
                      .++||+||+|.+......|+..||-..++|..|+|-.+.... ..  ....                             
T Consensus       250 ~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~av  329 (544)
T KOG0124|consen  250 GHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAV  329 (544)
T ss_pred             CccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCc
Confidence            899999999999999999999999999999999997665431 10  0000                             


Q ss_pred             ----C-----------------------------------Cccccc-------cccc-----------cc----------
Q psy3345         424 ----G-----------------------------------KVHCCI-------SERK-----------LD----------  436 (787)
Q Consensus       424 ----~-----------------------------------~~~~a~-------~~~~-----------~~----------  436 (787)
                          +                                   .++.++       +-+.           ++          
T Consensus       330 lg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eel  409 (544)
T KOG0124|consen  330 LGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEEL  409 (544)
T ss_pred             ccccCCccccCccccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhh
Confidence                0                                   000000       0000           00          


Q ss_pred             --------hh------------------hhhhhcCCCCEEEEeCC--CCCCC---HHHHHHhhccCCCeeEEEecCCC--
Q psy3345         437 --------AF------------------NQVVEARSKRIILVKNL--PYRTL---PTDLKALFEPFGDLGRVLVPPYG--  483 (787)
Q Consensus       437 --------~~------------------~~~~~~~~~~~i~v~nl--p~~~t---~~~l~~~F~~~G~v~~v~i~~~~--  483 (787)
                              .+                  ..--....+++|.++|+  |.+++   +.+|.+.|.+||.|.+|.|...+  
T Consensus       410 qpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~  489 (544)
T KOG0124|consen  410 QPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQG  489 (544)
T ss_pred             cccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccc
Confidence                    00                  00012335788999998  44443   56899999999999999987522  


Q ss_pred             c--------EEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccc
Q psy3345         484 I--------TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE  525 (787)
Q Consensus       484 ~--------~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~  525 (787)
                      .        --||+|....++.+|...|+|+.|.|+++..+.+.+..|..
T Consensus       490 e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~VvAE~YDQ~~FD~  539 (544)
T KOG0124|consen  490 EEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKVVAEVYDQERFDN  539 (544)
T ss_pred             cccchhhhheeeeeechhhHHHHHHHhhccceecCceeehhhhhhhcccc
Confidence            1        37999999999999999999999999999998887776643

>KOG0131|consensus

Probab=99.92  E-value=1.8e-24  Score=192.82  Aligned_cols=173  Identities=23%  Similarity=0.454  Sum_probs=154.3

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      .....+|||+||+..++++.|.++|-+.|+|.+++++++.-     ++...|||||+|.+.++|..|++-||...|.|++
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv-----~~~~qGygF~Ef~~eedadYAikiln~VkLYgrp   80 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRV-----TQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRP   80 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhh-----cccccceeEEEEechhhhHHHHHHHHHHHhcCce
Confidence            34568999999999999999999999999999999999876     5678999999999999999999999999999999


Q ss_pred             EEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEE-EeccccCCCCCCceEEEEEe
Q psy3345         657 IELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFV-RLPKKMVGSGLHRGFGFVEF  735 (787)
Q Consensus       657 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v-~i~~~~~~~g~~~g~afV~F  735 (787)
                      |+|..+.....             ....+.+|||+||.+++++.-|.+.|+.||.+.+. .|+++. .+|.++|||||.|
T Consensus        81 Irv~kas~~~~-------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~-~tg~~~~~g~i~~  146 (203)
T KOG0131|consen   81 IRVNKASAHQK-------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDP-DTGNPKGFGFINY  146 (203)
T ss_pred             eEEEecccccc-------------cccccccccccccCcchhHHHHHHHHHhccccccCCcccccc-cCCCCCCCeEEec
Confidence            99998873222             12235789999999999999999999999988663 788885 6799999999999


Q ss_pred             cCHHHHHHHHHHhcCCeeecCceEEEEEcccccc
Q psy3345         736 ITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       736 ~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~  769 (787)
                      .+.+.+.+|+.++| +..++.|++.|+||..++.
T Consensus       147 ~sfeasd~ai~s~n-gq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  147 ASFEASDAAIGSMN-GQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             hhHHHHHHHHHHhc-cchhcCCceEEEEEEecCC
Confidence            99999999999997 7999999999999986664

>KOG0147|consensus

Probab=99.91  E-value=6.5e-24  Score=220.67  Aligned_cols=275  Identities=23%  Similarity=0.344  Sum_probs=215.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      .+.++||+--|+..++..+|.++|+.+|+|.+|.++.|..+++++|.|||+|.+.+....|+ .|.|..+.|.+|.|...
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEeccc
Confidence            34578999999999999999999999999999999999999999999999999999999999 49999999999988764


Q ss_pred             CCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCH
Q psy3345         414 KPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQK  493 (787)
Q Consensus       414 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~  493 (787)
                      ...                                                                             
T Consensus       256 Eae-----------------------------------------------------------------------------  258 (549)
T KOG0147|consen  256 EAE-----------------------------------------------------------------------------  258 (549)
T ss_pred             HHH-----------------------------------------------------------------------------
Confidence            310                                                                             


Q ss_pred             HHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCccccccccccc
Q psy3345         494 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE  573 (787)
Q Consensus       494 ~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  573 (787)
                         +.. .+.....+.|.-                                                             
T Consensus       259 ---knr-~a~~s~a~~~k~-------------------------------------------------------------  273 (549)
T KOG0147|consen  259 ---KNR-AANASPALQGKG-------------------------------------------------------------  273 (549)
T ss_pred             ---HHH-HHhccccccccc-------------------------------------------------------------
Confidence               111 111111111100                                                             


Q ss_pred             ccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy3345         574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD  653 (787)
Q Consensus       574 ~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~  653 (787)
                        ...+...|||+||.++++++.|+.+|++||.|..|.+.++..     +|+++|||||+|.+.++|..|+..|||..|-
T Consensus       274 --~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~-----tG~skgfGfi~f~~~~~ar~a~e~lngfelA  346 (549)
T KOG0147|consen  274 --FTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSE-----TGRSKGFGFITFVNKEDARKALEQLNGFELA  346 (549)
T ss_pred             --cccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccc-----cccccCcceEEEecHHHHHHHHHHhccceec
Confidence              011223399999999999999999999999999999999875     7899999999999999999999999999999


Q ss_pred             CeEEEEEecCccccchh-----------------------hhhh-----------------------------------h
Q psy3345         654 EHQIELKRSNRNLESEA-----------------------TTVK-----------------------------------R  675 (787)
Q Consensus       654 g~~l~v~~~~~~~~~~~-----------------------~~~~-----------------------------------~  675 (787)
                      |+.|+|....-......                       ...+                                   +
T Consensus       347 Gr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~  426 (549)
T KOG0147|consen  347 GRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVR  426 (549)
T ss_pred             CceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcC
Confidence            99999976532111100                       0000                                   0


Q ss_pred             ccccccC-------CCCCEEEEecC--CccCc--------HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCH
Q psy3345         676 KSSNVAK-------QTGSKILVRNI--PFQAK--------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK  738 (787)
Q Consensus       676 ~~~~~~~-------~~~~~l~V~nL--p~~~t--------~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~  738 (787)
                      .....+.       .++.|+.++|+  |.+.|        .+||.+.|++||.|..|.+-++      +-|+.||.|.+.
T Consensus       427 ~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n------s~g~VYvrc~s~  500 (549)
T KOG0147|consen  427 VRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN------SAGCVYVRCPSA  500 (549)
T ss_pred             ccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC------CCceEEEecCcH
Confidence            0011122       45677888888  44333        3679999999999988888665      459999999999


Q ss_pred             HHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         739 NEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       739 ~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      +.|..|+.+|+ |++|.||-|...|-.
T Consensus       501 ~~A~~a~~alh-grWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  501 EAAGTAVKALH-GRWFAGRMITAKYLP  526 (549)
T ss_pred             HHHHHHHHHHh-hhhhccceeEEEEee
Confidence            99999999995 899999999998864

>KOG4212|consensus

Probab=99.91  E-value=1.4e-22  Score=203.03  Aligned_cols=239  Identities=21%  Similarity=0.214  Sum_probs=176.4

Q ss_pred             ccce-EEEecCcccCCCccCCHHHHHHHhhcc-CceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          11 PRNH-ISLLDLDEVEFIYKITQEQLKAKFEEK-GTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        11 ~~~~-~~~~~l~~~~lp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .+.| ++|.|     +||++.=+||++||..- |+|+-|.|+.|..|++||+|.|.|+++|.+++|++.||+..+.||.|
T Consensus        42 ~r~R~vfItN-----Ipyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l  116 (608)
T KOG4212|consen   42 ARDRSVFITN-----IPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGREL  116 (608)
T ss_pred             cccceEEEec-----CcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceE
Confidence            3445 99999     99999999999999866 79999999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCC
Q psy3345          89 KVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKD  168 (787)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (787)
                      .|.-...   .           ...                                        .+.            
T Consensus       117 ~vKEd~d---~-----------q~~----------------------------------------~~~------------  130 (608)
T KOG4212|consen  117 VVKEDHD---E-----------QRD----------------------------------------QYG------------  130 (608)
T ss_pred             EEeccCc---h-----------hhh----------------------------------------hhh------------
Confidence            9953321   0           000                                        000            


Q ss_pred             CCccccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCC
Q psy3345         169 GEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL  248 (787)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~  248 (787)
                                                                        ...|...++++.++-+.+-..-|..-|..-
T Consensus       131 --------------------------------------------------~~~r~g~~~f~~~~~~q~G~~~l~~~g~gg  160 (608)
T KOG4212|consen  131 --------------------------------------------------RIVRDGGGGFGGGGGVQGGNGGLNGGGGGG  160 (608)
T ss_pred             --------------------------------------------------heeeccCcccccCcceecccccccccCCCC
Confidence                                                              001223345666666666666666666555


Q ss_pred             CCcceeec-------ccceEEEeecChHhHHHHHhcCC-cccCCeeEEEeecccCCccccCCCcCCCCchhhhhhhhccc
Q psy3345         249 PLASVRTT-------FLGMAYIGFKDEKNCNKALNKNK-SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHW  320 (787)
Q Consensus       249 g~v~i~i~-------~~g~afV~F~~~~~A~~Al~~~~-~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (787)
                      |.+.--.+       +++..++.|.+.-.+..++.+-+ ....-+.++++                              
T Consensus       161 G~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~f------------------------------  210 (608)
T KOG4212|consen  161 GDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHIF------------------------------  210 (608)
T ss_pred             ccccCCCCcccccccccccCccccccccccchhhhcccchhhhhhhccCC------------------------------
Confidence            54311111       55677888887777777776322 22222223321                              


Q ss_pred             ccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCC
Q psy3345         321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG  400 (787)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~  400 (787)
                                 ..+...++||.||.+.+....|.+.|.-.|.|..|.+-.++. |.++|+|.++|.++-+|..|+..+++
T Consensus       211 -----------~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  211 -----------SPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             -----------CCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhcc
Confidence                       112233799999999999999999999999999999988865 78999999999999999999998887


Q ss_pred             ceeCCeEEEEee
Q psy3345         401 TVFLGRMLHLIP  412 (787)
Q Consensus       401 ~~~~g~~l~v~~  412 (787)
                      .-+..++..+..
T Consensus       279 ~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  279 QGLFDRRMTVRL  290 (608)
T ss_pred             CCCccccceeec
Confidence            666666555544

>KOG4307|consensus

Probab=99.90  E-value=1.3e-22  Score=214.00  Aligned_cols=192  Identities=13%  Similarity=0.040  Sum_probs=135.5

Q ss_pred             CCccceEEEeCCCCCCCHHhHHHhhcCCCCcceeec-------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecc
Q psy3345         221 KRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTT-------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYS  293 (787)
Q Consensus       221 ~~~~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~-------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~  293 (787)
                      ..+.+++.++++++++.+.|+++||.+.-+..+.|.       .+|.++|+|....++++|++++...+-.|++++-+  
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P--  385 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGP--  385 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecC--
Confidence            457799999999999999999999999866544433       47999999999999999999998888899999953  


Q ss_pred             cCCccccCCCcCCCC---chhhhhhhhccc--cc--ccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-
Q psy3345         294 KDNSAKYSGAADDNN---NASMENIKAKHW--KS--QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE-  365 (787)
Q Consensus       294 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-  365 (787)
                       ........+.....   ..........+.  .+  .............+.+|||..||..+++.++.++|.....|++ 
T Consensus       386 -~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~  464 (944)
T KOG4307|consen  386 -PGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDF  464 (944)
T ss_pred             -CCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhhe
Confidence             22211111110000   000000000000  00  0000011123345679999999999999999999998878888 


Q ss_pred             EEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         366 VILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       366 v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      |.|.+. -+++.++.|||.|..++++..|....+...++.|.|+|.....+
T Consensus       465 I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~  514 (944)
T KOG4307|consen  465 IELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADY  514 (944)
T ss_pred             eEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeechhhH
Confidence            555444 46888899999999999999998777777888899999877655

>KOG1365|consensus

Probab=99.90  E-value=1.4e-23  Score=206.96  Aligned_cols=284  Identities=14%  Similarity=0.208  Sum_probs=204.8

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEE-EEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ...|+.|+     |||..+..+|..||.+...... +-|+.+-.|+..|+|.|.|.++|.-..|+++ |+..+++|+|+|
T Consensus        60 ~vvvRaRg-----lpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryiev  133 (508)
T KOG1365|consen   60 NVVVRARG-----LPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEV  133 (508)
T ss_pred             ceEEEecC-----CCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceee
Confidence            34567777     9999999999999999954333 4555666899999999999999999999999 999999999999


Q ss_pred             EEccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCCC
Q psy3345          91 EKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGE  170 (787)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (787)
                      .-|..       .                                             +|+....+.+..          
T Consensus       134 Yka~g-------e---------------------------------------------~f~~iagg~s~e----------  151 (508)
T KOG1365|consen  134 YKATG-------E---------------------------------------------EFLKIAGGTSNE----------  151 (508)
T ss_pred             eccCc-------h---------------------------------------------hheEecCCcccc----------
Confidence            98775       1                                             122222221100          


Q ss_pred             ccccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCC--
Q psy3345         171 EKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL--  248 (787)
Q Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~--  248 (787)
                              .            +.                        -....+.-.|+++|||+++++.||.+||.+-  
T Consensus       152 --------~------------~~------------------------flsk~~qvivRmRGLPfdat~~dVv~FF~~~cp  187 (508)
T KOG1365|consen  152 --------A------------AP------------------------FLSKENQVIVRMRGLPFDATALDVVEFFGPPCP  187 (508)
T ss_pred             --------C------------CC------------------------CCCcccceEEEecCCCCCcchHHHHHhcCCCCc
Confidence                    0            00                        0112345579999999999999999999743  


Q ss_pred             ---CCcceeec------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecccCCcccc----CCCcCCCCchhhhhh
Q psy3345         249 ---PLASVRTT------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKY----SGAADDNNNASMENI  315 (787)
Q Consensus       249 ---g~v~i~i~------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~~~~~~~~----~~~~~~~~~~~~~~~  315 (787)
                         |.++|.++      .+|.|||.|..+++|+.||.+|+..|+-|||++++-........    ...+-.+...+... 
T Consensus       188 v~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~-  266 (508)
T KOG1365|consen  188 VTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLL-  266 (508)
T ss_pred             ccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCC-
Confidence               44466666      67999999999999999999999999999999974211111100    00000000000000 


Q ss_pred             hhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee---EEEEecCCCCCCcceEEEEEEcCHHHHH
Q psy3345         316 KAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLA---EVILPIDKETDKTKGFALVTFLMPEHAT  392 (787)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~---~v~i~~~~~~~~~~g~afV~F~~~~~A~  392 (787)
                           .  ..............||.+++|||.+|.++|.++|..|..-.   -|+|+.+. -|++.|.|||+|.+.++|.
T Consensus       267 -----p--~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~  338 (508)
T KOG1365|consen  267 -----P--GGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERAR  338 (508)
T ss_pred             -----C--CCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHH
Confidence                 0  00000111223366999999999999999999999986432   27888774 5999999999999999999


Q ss_pred             HHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         393 QAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       393 ~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      .|....+++.+.+|.|.|.++.-.
T Consensus       339 aaaqk~hk~~mk~RYiEvfp~S~e  362 (508)
T KOG1365|consen  339 AAAQKCHKKLMKSRYIEVFPCSVE  362 (508)
T ss_pred             HHHHHHHHhhcccceEEEeeccHH
Confidence            999988888888999999998754

>KOG0146|consensus

Probab=99.86  E-value=2.3e-21  Score=182.42  Aligned_cols=183  Identities=23%  Similarity=0.370  Sum_probs=155.5

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCC-ccCC--e
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNS-SLDE--H  655 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~-~l~g--~  655 (787)
                      ..+.|||+-|...-.+++++.+|..||.|.+|.+.+.++      +.++|++||.|.++.+|+.||..|||. .+-|  .
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d------g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASS   91 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD------GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASS   91 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC------CCCCCceEEEeccchHHHHHHHHhcccccCCCCcc
Confidence            568999999999999999999999999999999999877      789999999999999999999999995 4545  6


Q ss_pred             EEEEEecCccccchhhh---------------------------------------------------------------
Q psy3345         656 QIELKRSNRNLESEATT---------------------------------------------------------------  672 (787)
Q Consensus       656 ~l~v~~~~~~~~~~~~~---------------------------------------------------------------  672 (787)
                      .|.|++++...+.....                                                               
T Consensus        92 SLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~a  171 (371)
T KOG0146|consen   92 SLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNA  171 (371)
T ss_pred             ceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhh
Confidence            89999987432210000                                                               


Q ss_pred             -----------h---h----------------------------------------------------------------
Q psy3345         673 -----------V---K----------------------------------------------------------------  674 (787)
Q Consensus       673 -----------~---~----------------------------------------------------------------  674 (787)
                                 +   .                                                                
T Consensus       172 ngl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~  251 (371)
T KOG0146|consen  172 NGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQ  251 (371)
T ss_pred             cccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHH
Confidence                       0   0                                                                


Q ss_pred             -----------------------hccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEE
Q psy3345         675 -----------------------RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG  731 (787)
Q Consensus       675 -----------------------~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~a  731 (787)
                                             -.........+|+|||.+||.+..+.+|.++|-.||.|++.++..|. -++++++||
T Consensus       252 ~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDR-ATNQSKCFG  330 (371)
T KOG0146|consen  252 QYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDR-ATNQSKCFG  330 (371)
T ss_pred             HHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehh-cccccccee
Confidence                                   00000114478999999999999999999999999999999998886 789999999


Q ss_pred             EEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccccc
Q psy3345         732 FVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       732 fV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~  769 (787)
                      ||.|+++-+|+.||++|| |..++-++|+|.+.+|++.
T Consensus       331 FVSfDNp~SaQaAIqAMN-GFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  331 FVSFDNPASAQAAIQAMN-GFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             eEecCCchhHHHHHHHhc-chhhhhhhhhhhhcCcccc
Confidence            999999999999999997 7999999999999998874

>KOG0131|consensus

Probab=99.84  E-value=1.2e-20  Score=168.43  Aligned_cols=165  Identities=20%  Similarity=0.279  Sum_probs=146.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC------CcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEec
Q psy3345         446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  519 (787)
Q Consensus       446 ~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  519 (787)
                      ...+|+|.||+..++++-|+++|-+.|+|..+.+|++      .|+|||+|.++++|.-|++-|+...++|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            4688999999999999999999999999999999973      4799999999999999999999999999999999885


Q ss_pred             CccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHH
Q psy3345         520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  599 (787)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~  599 (787)
                      ..                                                    ......+.+|||+||.+.+++..|.+
T Consensus        88 ~~----------------------------------------------------~~nl~vganlfvgNLd~~vDe~~L~d  115 (203)
T KOG0131|consen   88 AH----------------------------------------------------QKNLDVGANLFVGNLDPEVDEKLLYD  115 (203)
T ss_pred             cc----------------------------------------------------cccccccccccccccCcchhHHHHHH
Confidence            22                                                    11123357999999999999999999


Q ss_pred             HHhhcCCeEE-EEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCcccc
Q psy3345         600 HFKKCGPIAS-VTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE  667 (787)
Q Consensus       600 ~F~~~G~v~~-v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~  667 (787)
                      .|+.||.+.+ -+++++++     ++.++|||||.|.+.+.+.+|+..|||..+..+++.|.++.++..
T Consensus       116 tFsafG~l~~~P~i~rd~~-----tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  116 TFSAFGVLISPPKIMRDPD-----TGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHhccccccCCccccccc-----CCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            9999998755 56777766     778999999999999999999999999999999999999876543

>KOG1456|consensus

Probab=99.83  E-value=1.2e-17  Score=164.79  Aligned_cols=380  Identities=17%  Similarity=0.163  Sum_probs=256.1

Q ss_pred             cCCCccceEEEeCCCCCCCHHhHHHhhcCCCCcce-eec-ccceEEEeecChHhHHHHHhc---CCcccCCeeEEEeecc
Q psy3345         219 VHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASV-RTT-FLGMAYIGFKDEKNCNKALNK---NKSFWKGKQLNIYKYS  293 (787)
Q Consensus       219 ~~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v~i-~i~-~~g~afV~F~~~~~A~~Al~~---~~~~l~g~~i~v~~~~  293 (787)
                      .....+-+|+|++|-..++|.||.+.++.+|.+.. ... .+..|.|+|.+.+-|..++..   +..++.|+.-.+-   
T Consensus        26 hk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~N---  102 (494)
T KOG1456|consen   26 HKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFN---  102 (494)
T ss_pred             CCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcc---
Confidence            34455678999999999999999999999999843 333 778999999999999999884   3455555443331   


Q ss_pred             cCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEE--EcCCCCCCCHHHHHHHHHhcCCeeEEEEecC
Q psy3345         294 KDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIF--VRNLSYTVTEDDLTKLFEKYGPLAEVILPID  371 (787)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~  371 (787)
                                     .+.........          .+...++..|.  |-|--|.+|-+-|..+....|+|..|.|.+.
T Consensus       103 ---------------yStsq~i~R~g----------~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk  157 (494)
T KOG1456|consen  103 ---------------YSTSQCIERPG----------DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK  157 (494)
T ss_pred             ---------------cchhhhhccCC----------CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec
Confidence                           00011110000          11122233344  4565678999999999999999999988753


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEeeCCCCCC------CCCCC------------CCc-----
Q psy3345         372 KETDKTKGFALVTFLMPEHATQAYQHLDGTVFLG--RMLHLIPGKPKEN------EGNVD------------GKV-----  426 (787)
Q Consensus       372 ~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g--~~l~v~~~~~~~~------~~~~~------------~~~-----  426 (787)
                        +|   =.|.|+|.+.+.|++|...|||..|..  -+|+|.++++...      .+..+            +..     
T Consensus       158 --ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~  232 (494)
T KOG1456|consen  158 --NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQ  232 (494)
T ss_pred             --cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccc
Confidence              33   269999999999999999999987743  5777788776410      00000            000     


Q ss_pred             ----------------------------------cccccccccchhhhhhhcCCCCEEEEeCCCCC-CCHHHHHHhhccC
Q psy3345         427 ----------------------------------HCCISERKLDAFNQVVEARSKRIILVKNLPYR-TLPTDLKALFEPF  471 (787)
Q Consensus       427 ----------------------------------~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~-~t~~~l~~~F~~~  471 (787)
                                                        |...+.........+....+..++.|.+|... ++-+.|.++|-.|
T Consensus       233 ~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClY  312 (494)
T KOG1456|consen  233 RQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLY  312 (494)
T ss_pred             cCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhc
Confidence                                              00000000001112234556889999999865 6889999999999


Q ss_pred             CCeeEEEecCCC-cEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhh
Q psy3345         472 GDLGRVLVPPYG-ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKK  550 (787)
Q Consensus       472 G~v~~v~i~~~~-~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  550 (787)
                      |.|.+|.+.+.+ +.|.|++.++.+.++|+..||+..+.|.+|.+.++.+.....- ..          -..+.+.    
T Consensus       313 GNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~-~p----------flLpDgS----  377 (494)
T KOG1456|consen  313 GNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPV-QP----------FLLPDGS----  377 (494)
T ss_pred             CceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccC-Cc----------eecCCCC----
Confidence            999999998854 7999999999999999999999999999999988866632221 00          0011000    


Q ss_pred             cccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCC-eEEEEEeecCCCCCCCCCCcccE
Q psy3345         551 ENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQFLSMGY  629 (787)
Q Consensus       551 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~-v~~v~i~~~~~~~~~~~~~s~G~  629 (787)
                       ....+...+.........+...+.-..+.++|..-|-|..+|++.|.++|...+. -.++++..-+.       .-..-
T Consensus       378 -pSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~ks-------erSss  449 (494)
T KOG1456|consen  378 -PSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLKS-------ERSSS  449 (494)
T ss_pred             -cchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeecccc-------ccccc
Confidence             0111111111111111111122344567889999999999999999999987664 45666654332       23346


Q ss_pred             EEEEeCCHHHHHHHHHHhCCCccCC
Q psy3345         630 GFVQFYTRESLNQALKVLQNSSLDE  654 (787)
Q Consensus       630 afV~F~~~e~A~~A~~~lng~~l~g  654 (787)
                      |.++|.+.++|..|+..+|...+.+
T Consensus       450 GllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  450 GLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             ceeeeehHHHHHHHHHHhccccccC
Confidence            8999999999999999999988865

>KOG0109|consensus

Probab=99.82  E-value=3e-20  Score=177.65  Aligned_cols=146  Identities=24%  Similarity=0.455  Sum_probs=136.7

Q ss_pred             CeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Q psy3345         581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK  660 (787)
Q Consensus       581 ~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~  660 (787)
                      ..|||+|||..+++.+|+.+|++||.|..|.|++             -||||...+...|..|+..|||..|+|..|.|.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK-------------NYgFVHiEdktaaedairNLhgYtLhg~nInVe   69 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK-------------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVE   69 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec-------------ccceEEeecccccHHHHhhcccceecceEEEEE
Confidence            4699999999999999999999999999999996             389999999999999999999999999999998


Q ss_pred             ecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHH
Q psy3345         661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE  740 (787)
Q Consensus       661 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~  740 (787)
                      -++.+..                ..++|+|.||.+..+.++|+..|++||.|..++|.++         |+||.|.-.++
T Consensus        70 aSksKsk----------------~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd---------y~fvh~d~~ed  124 (346)
T KOG0109|consen   70 ASKSKSK----------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD---------YAFVHFDRAED  124 (346)
T ss_pred             eccccCC----------------CccccccCCCCccccCHHHhhhhcccCCceeeeeecc---------eeEEEEeeccc
Confidence            8775533                6789999999999999999999999999999999877         79999999999


Q ss_pred             HHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         741 AKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       741 A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      |..|+..|+ ++.|.|++|+|....
T Consensus       125 a~~air~l~-~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen  125 AVEAIRGLD-NTEFQGKRMHVQLST  148 (346)
T ss_pred             hHHHHhccc-ccccccceeeeeeec
Confidence            999999998 599999999999875

>KOG0109|consensus

Probab=99.79  E-value=3.4e-19  Score=170.45  Aligned_cols=150  Identities=23%  Similarity=0.411  Sum_probs=138.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccc
Q psy3345         448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAK  527 (787)
Q Consensus       448 ~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~  527 (787)
                      ..+||.|||..+++.+|+.+|++||.|..|.|.+  ++|||...+...|..|+..|+|..+.|..|.|+-+..+      
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK------   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK------   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--ccceEEeecccccHHHHhhcccceecceEEEEEecccc------
Confidence            3589999999999999999999999999999984  58999999999999999999999999999999977444      


Q ss_pred             cccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCe
Q psy3345         528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI  607 (787)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v  607 (787)
                                                                       ....+.|+|+||.+.++..+|+..|++||+|
T Consensus        75 -------------------------------------------------sk~stkl~vgNis~tctn~ElRa~fe~ygpv  105 (346)
T KOG0109|consen   75 -------------------------------------------------SKASTKLHVGNISPTCTNQELRAKFEKYGPV  105 (346)
T ss_pred             -------------------------------------------------CCCccccccCCCCccccCHHHhhhhcccCCc
Confidence                                                             2346789999999999999999999999999


Q ss_pred             EEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCcccc
Q psy3345         608 ASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE  667 (787)
Q Consensus       608 ~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~  667 (787)
                      ..|.|.+             +|+||.|.-.++|..|++.|+|..++|+++.|+++.....
T Consensus       106 iecdivk-------------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen  106 IECDIVK-------------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             eeeeeec-------------ceeEEEEeeccchHHHHhcccccccccceeeeeeeccccc
Confidence            9999986             6999999999999999999999999999999999876544

>KOG0146|consensus

Probab=99.78  E-value=1.4e-18  Score=163.72  Aligned_cols=87  Identities=20%  Similarity=0.293  Sum_probs=80.6

Q ss_pred             ccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy3345         574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD  653 (787)
Q Consensus       574 ~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~  653 (787)
                      .....++|+|||.+||.+..+.+|...|-+||.|.+.++..|+.     +..|++||||.|.++.+|+.||.+|||+.|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRA-----TNQSKCFGFVSfDNp~SaQaAIqAMNGFQIG  353 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRA-----TNQSKCFGFVSFDNPASAQAAIQAMNGFQIG  353 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhc-----cccccceeeEecCCchhHHHHHHHhcchhhh
Confidence            34567789999999999999999999999999999999999987     7899999999999999999999999999999


Q ss_pred             CeEEEEEecCcc
Q psy3345         654 EHQIELKRSNRN  665 (787)
Q Consensus       654 g~~l~v~~~~~~  665 (787)
                      -++|+|.+..++
T Consensus       354 MKRLKVQLKRPk  365 (371)
T KOG0146|consen  354 MKRLKVQLKRPK  365 (371)
T ss_pred             hhhhhhhhcCcc
Confidence            999999886544

>KOG4307|consensus

Probab=99.75  E-value=4.9e-17  Score=172.22  Aligned_cols=531  Identities=12%  Similarity=0.014  Sum_probs=285.0

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCc-ceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKF-RRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~-~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      -.+.+.+     +++++++.|+++||.+. .|..++|..++-+.+ +|-++|.|....++++|+++ |.+.+-.|+|+|.
T Consensus       312 ~y~~~~g-----m~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~  384 (944)
T KOG4307|consen  312 YYNNYKG-----MEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTG  384 (944)
T ss_pred             heeeecc-----cccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-Cchhhhhcceeec
Confidence            3466777     99999999999999998 578899999885554 99999999999999999999 9999999999998


Q ss_pred             EccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCCCc
Q psy3345          92 KCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDGEE  171 (787)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (787)
                      ++..       +.|......- +.                                      ..+..-+ ....+..+- 
T Consensus       385 P~g~-------~~~~~a~~~~-~~--------------------------------------~~~~~~~-~~hg~p~~~-  416 (944)
T KOG4307|consen  385 PPGN-------LGRNGAPPFQ-AG--------------------------------------VPPPVIQ-NNHGRPIAP-  416 (944)
T ss_pred             CCCc-------cccccCcccc-cc--------------------------------------CCCCccc-ccCCCCCCC-
Confidence            8876       3342211100 00                                      0000000 000000000 


Q ss_pred             cccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCCCCc
Q psy3345         172 KEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA  251 (787)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v  251 (787)
                                                 .++..      ...+.  .+.......+|||..||..+++.++.++|.....|
T Consensus       417 ---------------------------pr~~~------~~gq~--vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~V  461 (944)
T KOG4307|consen  417 ---------------------------PRAMV------RPGQN--VPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAV  461 (944)
T ss_pred             ---------------------------ccccc------CCCCC--CCCCCCccceEEeccCCccccccchhhhhhhhhhh
Confidence                                       00000      00000  11334556899999999999999999999998766


Q ss_pred             -c-eeec------ccceEEEeecChHhHHHHHh-cCCcccCCeeEEEeecccCCccccCCCcCCCCchhhhhhhhccccc
Q psy3345         252 -S-VRTT------FLGMAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKS  322 (787)
Q Consensus       252 -~-i~i~------~~g~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  322 (787)
                       + |.|.      .++.|||.|..++++.+|+. .++.+++.+.|.|..+++..+......        +....-...  
T Consensus       462 ed~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m~~ek~~--------~~~~~lq~~--  531 (944)
T KOG4307|consen  462 EDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAMMMEKNG--------EQGIKLQQS--  531 (944)
T ss_pred             hheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhHHHHHHHhH--------HHHHHHhhh--
Confidence             4 5555      44799999999988888888 889999999999976555444110000        000000000  


Q ss_pred             ccchhhhhc--c----cCCCCeEEEcCCC-CCCCHHHHHHHHHhcCCeeE---EEEecCCCCCCcceEEEEEEcCHHHHH
Q psy3345         323 QEDSVQFAE--D----IAESGRIFVRNLS-YTVTEDDLTKLFEKYGPLAE---VILPIDKETDKTKGFALVTFLMPEHAT  392 (787)
Q Consensus       323 ~~~~~~~~~--~----~~~~~~l~V~nLp-~~~te~~l~~~F~~~G~i~~---v~i~~~~~~~~~~g~afV~F~~~~~A~  392 (787)
                      ..++.+...  .    .....+-.+.+.+ ++.+....+....  +.+.+   ..+..| ..+.+.+-+||.|.+...+.
T Consensus       532 ~~dqre~~l~~p~~~v~~~~~~~~~~~~~~F~~~~rr~~~e~~--~~~~~~n~~p~~~d-N~~~~~~~~~v~~~n~p~~r  608 (944)
T KOG4307|consen  532 DKDQRETALDGPIPSVSMVPSKEQRSHEDDFDKKSRRSRWENT--SPIRSPNRSPLRRD-NRDRSRSRSPVRRRNSPRRR  608 (944)
T ss_pred             hhHHHHHhhcCCccchhhhhhhhhhccCcccccchHHHHhhhc--CCccCccccccccc-cCCcccccCccccCCCcccc
Confidence            000000000  0    0011223344555 5666655544333  33333   334444 34778889999999888777


Q ss_pred             HHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCC
Q psy3345         393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG  472 (787)
Q Consensus       393 ~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G  472 (787)
                      .-.. ++...+.++.....--...+...+.++.+...-.-   -  ......+.-.-+.+..|+- +..-+|..+|.  |
T Consensus       609 ~~~~-~~~~~vnn~pF~m~~~~~~~~~sekn~Pa~~~~~~---~--~gv~~~p~v~~~~~~~l~~-~r~~~~g~l~t--g  679 (944)
T KOG4307|consen  609 EEHT-RWCVQVNNVPFRMKDEELLEWFSEKNRPAKLTRTF---Y--DGVASDPWVAEFSSESLMK-RRSFGIGTLCT--G  679 (944)
T ss_pred             chhh-hhhhcccCcceeecchhhhhhhcccCCcccccccc---c--CCCCCCccccccccccccc-ccCCCcccccc--C
Confidence            6653 44445555553332111101100000000000000   0  0000000000111111111 00111222222  1


Q ss_pred             CeeEEE-e-------cCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccc---------cccccccc
Q psy3345         473 DLGRVL-V-------PPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAK---------EKSKGKEK  535 (787)
Q Consensus       473 ~v~~v~-i-------~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~---------~~~~~~~~  535 (787)
                      .-.++. +       ...-+..+++|.+....+.|+.....+.+.+..+.+--+...-.....         ........
T Consensus       680 ~~lr~~~i~~~~~~~~~~~g~~~~e~~~~~~ee~a~~~~~~~~an~~~~fn~p~~~~gs~~~~p~~p~p~~~gg~nG~~~  759 (944)
T KOG4307|consen  680 RTLRLRYIDNAKADEILKIGDVYGEGKRQMNEEAALQHEVAEKANPPSFFNAPAATRGSGPMPPLNPAPLPSGGQNGMNV  759 (944)
T ss_pred             cccccchhhhhhhccccccccceeccCCccchhHHHHHHhhhhccCCCcccccccccccCCCCCCCCCCCCCCccCCCCC
Confidence            000000 0       112346789999999999999998888888777765433211000000         00000000


Q ss_pred             cccc----------ccc-------------c---cchhhhhc---cccc--cc----ccCCC------------------
Q psy3345         536 EKNE----------EEG-------------E---EGEEEKKE---NTAE--ED----NQQGV------------------  562 (787)
Q Consensus       536 ~~~~----------~~~-------------~---~~~~~~~~---~~~~--~~----~~~~~------------------  562 (787)
                      +...          ...             +   .+......   ....  .+    ..++.                  
T Consensus       760 p~pn~~NdGapg~g~~vp~~f~~gp~~~~gp~g~gggP~~~qngP~sl~~~p~~~f~sn~p~~~gf~pg~rggpp~~g~g  839 (944)
T KOG4307|consen  760 PPPNGFNDGAPGRGGFVPRGFSQGPGMGRGPHGGGGGPNFYQNGPNSLNNGPQGQFRSNQPNDGGFRPGFRGGPPGRGGG  839 (944)
T ss_pred             CCCCCCCCCCCCcCCcCCccccCCCCCCCCCCCCCCCccccccCCcccCCCCccccCCCCCCcCCcCCccCCCCCCCCCC
Confidence            0000          000             0   00000000   0000  00    00000                  


Q ss_pred             cc-------ccccccc--ccccCCCCC-CeEEecCCCCCCCHHHHHHHHhhcCCeEE-EEEeecCCCCCCCCCCcccEEE
Q psy3345         563 PE-------VEENVEE--DEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIAS-VTVARKKDPKSPGQFLSMGYGF  631 (787)
Q Consensus       563 ~~-------~~~~~~~--~~~~~~~~~-~~l~V~NLp~~~t~~~L~~~F~~~G~v~~-v~i~~~~~~~~~~~~~s~G~af  631 (787)
                      +.       .....-.  -......++ +.|.+.|+|++++.++|.++|..|-.+-. +.+.++.      .|..+|-|.
T Consensus       840 pg~~~g~~p~~~~~P~~~~~~~~~~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd------~G~pTGe~m  913 (944)
T KOG4307|consen  840 PGGFQGGSPGDDSQPSQELMELIKSPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRND------DGVPTGECM  913 (944)
T ss_pred             CCCCCCCCCCCCCCChHHHHHhcCCCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecC------CCCccccee
Confidence            00       0000000  001122233 48999999999999999999999987644 4444433      488999999


Q ss_pred             EEeCCHHHHHHHHHHhCCCccCCeEEEEEe
Q psy3345         632 VQFYTRESLNQALKVLQNSSLDEHQIELKR  661 (787)
Q Consensus       632 V~F~~~e~A~~A~~~lng~~l~g~~l~v~~  661 (787)
                      |-|.+.++|.+|...|+++.|..+.+.+.+
T Consensus       914 vAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  914 VAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            999999999999999999999999998865

>KOG1365|consensus

Probab=99.74  E-value=2e-18  Score=170.74  Aligned_cols=274  Identities=19%  Similarity=0.221  Sum_probs=191.0

Q ss_pred             CccceEEEeCCCCCCCHHhHHHhhcCCCCc--ceeec------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecc
Q psy3345         222 RQYHTIVVKNLPAGVKKKDLKAYFKPLPLA--SVRTT------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYS  293 (787)
Q Consensus       222 ~~~~~v~v~nLp~~~te~di~~~F~~~g~v--~i~i~------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~  293 (787)
                      .++..|+.++||+..+..+|..||+...+.  .+-|+      ..|+|.|.|.+++.-..|+++|+..+++++|+|++..
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~  137 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKAT  137 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccC
Confidence            457789999999999999999999998655  23333      5689999999999999999999999999999998533


Q ss_pred             cCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhc----CCeeEEEEe
Q psy3345         294 KDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKY----GPLAEVILP  369 (787)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~  369 (787)
                      ..+.......         .......+.          .....-.|.+++||+++|+.++.++|.+-    |....|.++
T Consensus       138 ge~f~~iagg---------~s~e~~~fl----------sk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV  198 (508)
T KOG1365|consen  138 GEEFLKIAGG---------TSNEAAPFL----------SKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFV  198 (508)
T ss_pred             chhheEecCC---------ccccCCCCC----------CcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEE
Confidence            3333321110         000000000          01112358899999999999999999632    234455555


Q ss_pred             cCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCC---------CCccccccccccchhhh
Q psy3345         370 IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVD---------GKVHCCISERKLDAFNQ  440 (787)
Q Consensus       370 ~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~---------~~~~~a~~~~~~~~~~~  440 (787)
                      .. ..|+.+|-|||.|..+++|+.|+. .|...|+-|+|.+..+...+.....+         +.....+...   ....
T Consensus       199 ~r-pdgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~---p~~~  273 (508)
T KOG1365|consen  199 TR-PDGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGG---PARL  273 (508)
T ss_pred             EC-CCCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCC---cccc
Confidence            54 359999999999999999999997 57778888998887665432110000         0000000000   0011


Q ss_pred             hhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCee---EEEe--cC---CCcEEEEEeCCHHHHHHHHHHhcCCeeCCee
Q psy3345         441 VVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLG---RVLV--PP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVP  512 (787)
Q Consensus       441 ~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~---~v~i--~~---~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~  512 (787)
                      ......+.+|.+++||+.++.++|.++|..|..-.   -|.+  ..   ..|.|||+|.+++.|..|..+.+.+...+|.
T Consensus       274 ~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RY  353 (508)
T KOG1365|consen  274 VPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRY  353 (508)
T ss_pred             CCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccce
Confidence            22344588999999999999999999999887532   1333  32   2257999999999999999998888777887


Q ss_pred             EEEEEec
Q psy3345         513 LYLEWAP  519 (787)
Q Consensus       513 l~v~~~~  519 (787)
                      |.|-.+.
T Consensus       354 iEvfp~S  360 (508)
T KOG1365|consen  354 IEVFPCS  360 (508)
T ss_pred             EEEeecc
Confidence            7776553

>KOG0120|consensus

Probab=99.74  E-value=1.6e-17  Score=176.54  Aligned_cols=292  Identities=19%  Similarity=0.280  Sum_probs=211.2

Q ss_pred             cCCCccceEEEeCCCCCCCHHhHHHhhcCC-----------CC--cceeec-ccceEEEeecChHhHHHHHhcCCcccCC
Q psy3345         219 VHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-----------PL--ASVRTT-FLGMAYIGFKDEKNCNKALNKNKSFWKG  284 (787)
Q Consensus       219 ~~~~~~~~v~v~nLp~~~te~di~~~F~~~-----------g~--v~i~i~-~~g~afV~F~~~~~A~~Al~~~~~~l~g  284 (787)
                      ...+..+.++|.++|+.++++....||...           |.  +.+.+. .+++||++|.+.++|..|+.+++..+.|
T Consensus       170 ~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g  249 (500)
T KOG0120|consen  170 QATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAMALDGIIFEG  249 (500)
T ss_pred             chhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhhcccchhhCC
Confidence            456788999999999999999999999875           11  133333 6789999999999999999999999999


Q ss_pred             eeEEEeecccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee
Q psy3345         285 KQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLA  364 (787)
Q Consensus       285 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~  364 (787)
                      +.+.+..  +......+.......   ....-...|.       ..........+||++||...++.++.++...||++.
T Consensus       250 ~~~~~~r--~~d~~~~p~~~~~~~---~~~~~~~~~~-------~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk  317 (500)
T KOG0120|consen  250 RPLKIRR--PHDYQPVPGITLSPS---QLGKVGLLPA-------STDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLK  317 (500)
T ss_pred             CCceecc--cccccCCccchhhhc---cccccCCccc-------ccCcccccchhhhccCcCccCHHHHHHHHHhcccch
Confidence            9998852  111111000000000   0000000111       112334566899999999999999999999999999


Q ss_pred             EEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCC--ccccccccccchhhhhh
Q psy3345         365 EVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGK--VHCCISERKLDAFNQVV  442 (787)
Q Consensus       365 ~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~--~~~a~~~~~~~~~~~~~  442 (787)
                      ...++.+..+|.++||||.+|.++.....|+..|||..++++.|.|..+-...........  ... .  ..+.......
T Consensus       318 ~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~-~--~~i~~~~~q~  394 (500)
T KOG0120|consen  318 AFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQ-V--PGIPLLMTQM  394 (500)
T ss_pred             hheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccc-c--ccchhhhccc
Confidence            9999999999999999999999999999999999999999999999987765211110000  000 0  0011111122


Q ss_pred             hcCCCCEEEEeCCC--CCC--------CHHHHHHhhccCCCeeEEEecCC---------CcEEEEEeCCHHHHHHHHHHh
Q psy3345         443 EARSKRIILVKNLP--YRT--------LPTDLKALFEPFGDLGRVLVPPY---------GITGLVEFLQKNQAKAAFNSL  503 (787)
Q Consensus       443 ~~~~~~~i~v~nlp--~~~--------t~~~l~~~F~~~G~v~~v~i~~~---------~~~a~V~F~~~~~A~~A~~~l  503 (787)
                      ...++.++.+.|+=  .+.        -.++++..|++||.|.+|.++..         -|..||+|.+.+++++|.+.|
T Consensus       395 ~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L  474 (500)
T KOG0120|consen  395 AGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEEL  474 (500)
T ss_pred             CCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHc
Confidence            34556666666652  111        12567788999999999999864         246999999999999999999


Q ss_pred             cCCeeCCeeEEEEEecCccccc
Q psy3345         504 AYTKFKEVPLYLEWAPEGVFAE  525 (787)
Q Consensus       504 ~~~~~~g~~l~v~~~~~~~~~~  525 (787)
                      +|+.|.+|+|...|.++..|..
T Consensus       475 ~GrKF~nRtVvtsYydeDkY~~  496 (500)
T KOG0120|consen  475 TGRKFANRTVVASYYDEDKYHA  496 (500)
T ss_pred             cCceeCCcEEEEEecCHHHhhc
Confidence            9999999999999998775543

>KOG4205|consensus

Probab=99.73  E-value=9.1e-18  Score=170.46  Aligned_cols=176  Identities=24%  Similarity=0.419  Sum_probs=153.5

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEE
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE  658 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~  658 (787)
                      ..+.|||++|+.+++++.|+++|++||.|..|.+++++.     +++++||+||+|++++...+++. .-.+.|+|+.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~-----t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve   78 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPS-----TGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVE   78 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCC-----CCCcccccceecCCCcchheeec-ccccccCCcccc
Confidence            568999999999999999999999999999999999987     58999999999999999988887 446789999999


Q ss_pred             EEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCH
Q psy3345         659 LKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK  738 (787)
Q Consensus       659 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~  738 (787)
                      ++.+.+.......        .......+|||.+||..+++.+++++|.+||.|..+-++.+. .+.+++|||||.|.+.
T Consensus        79 ~k~av~r~~~~~~--------~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~-~~~~~rgFgfv~~~~e  149 (311)
T KOG4205|consen   79 PKRAVSREDQTKV--------GRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDK-TTSRPRGFGFVTFDSE  149 (311)
T ss_pred             ceeccCccccccc--------ccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecc-cccccccceeeEeccc
Confidence            9887654431110        111256789999999999999999999999999999999986 7899999999999999


Q ss_pred             HHHHHHHHHhcCCeeecCceEEEEEccccccHH
Q psy3345         739 NEAKRAMKALCQSTHLYGRRLVLEWAEEADNVE  771 (787)
Q Consensus       739 ~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~~  771 (787)
                      +...+++..-  .+.|+|+.+.|.-|.|++...
T Consensus       150 ~sVdkv~~~~--f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  150 DSVDKVTLQK--FHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             cccceecccc--eeeecCceeeEeeccchhhcc
Confidence            9999998864  689999999999999998754

>KOG0120|consensus

Probab=99.72  E-value=9.5e-17  Score=170.62  Aligned_cols=289  Identities=18%  Similarity=0.292  Sum_probs=211.9

Q ss_pred             hcCCCCEEEEeCCCCCCCHHHHHHhhccC-----------C-CeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC
Q psy3345         443 EARSKRIILVKNLPYRTLPTDLKALFEPF-----------G-DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE  510 (787)
Q Consensus       443 ~~~~~~~i~v~nlp~~~t~~~l~~~F~~~-----------G-~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g  510 (787)
                      .......++|.++|+.++++.+..+|..-           | .+..+.+....++|+++|.+.++|..|+. +++..+.|
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g  249 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAMA-LDGIIFEG  249 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhhc-ccchhhCC
Confidence            34456789999999999999999888753           3 26788888889999999999999999976 78888889


Q ss_pred             eeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCC
Q psy3345         511 VPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNF  590 (787)
Q Consensus       511 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~  590 (787)
                      .++.+..-..............             +                 ...................++|+|||.
T Consensus       250 ~~~~~~r~~d~~~~p~~~~~~~-------------~-----------------~~~~~~~~~~t~~~~~~~ki~v~~lp~  299 (500)
T KOG0120|consen  250 RPLKIRRPHDYQPVPGITLSPS-------------Q-----------------LGKVGLLPASTDVPDSPNKIFVGGLPL  299 (500)
T ss_pred             CCceecccccccCCccchhhhc-------------c-----------------ccccCCcccccCcccccchhhhccCcC
Confidence            8887754322210000000000             0                 000000111122344567899999999


Q ss_pred             CCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchh
Q psy3345         591 NSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA  670 (787)
Q Consensus       591 ~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~  670 (787)
                      ..++.++.++...||.+...++..+..     ++.++||||.+|.++.-...|+..|||..+++..|.|+.+........
T Consensus       300 ~l~~~q~~Ell~~fg~lk~f~lv~d~~-----~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~  374 (500)
T KOG0120|consen  300 YLTEDQVKELLDSFGPLKAFRLVKDSA-----TGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNAN  374 (500)
T ss_pred             ccCHHHHHHHHHhcccchhheeecccc-----cccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhcc
Confidence            999999999999999999999999876     588999999999999999999999999999999999998876544211


Q ss_pred             hhhh----------hccccccCCCCCEEEEecC--CccCc--------HHHHHHHHHhcCCeeEEEecccc--CCCCCCc
Q psy3345         671 TTVK----------RKSSNVAKQTGSKILVRNI--PFQAK--------QSEVEELFKAFGELKFVRLPKKM--VGSGLHR  728 (787)
Q Consensus       671 ~~~~----------~~~~~~~~~~~~~l~V~nL--p~~~t--------~~dL~~~F~~~G~I~~v~i~~~~--~~~g~~~  728 (787)
                      ....          .........+...|.+.|+  |.+..        -++++.-|++||.|.+|.|++..  .......
T Consensus       375 ~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~  454 (500)
T KOG0120|consen  375 VNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGT  454 (500)
T ss_pred             ccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCc
Confidence            1100          0001222345566666666  22222        24588888899999999999883  1123345


Q ss_pred             eEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         729 GFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       729 g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      |-.||+|.+.++|++|+.+|+ |+.|.||.++.+|-.+++
T Consensus       455 GkVFVefas~ed~qrA~~~L~-GrKF~nRtVvtsYydeDk  493 (500)
T KOG0120|consen  455 GKVFVEFADTEDSQRAMEELT-GRKFANRTVVASYYDEDK  493 (500)
T ss_pred             ccEEEEecChHHHHHHHHHcc-CceeCCcEEEEEecCHHH
Confidence            678999999999999999996 899999999999987654

>KOG0105|consensus

Probab=99.70  E-value=3.6e-16  Score=139.76  Aligned_cols=156  Identities=17%  Similarity=0.331  Sum_probs=129.7

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEE
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE  658 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~  658 (787)
                      ..+.|||+|||.++-+.+|.++|.+||.|..+.+...+.        .-+||||+|.++-+|..|+..-+|..++|+.|+
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g--------~ppfafVeFEd~RDAeDAiygRdGYdydg~rLR   76 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPG--------PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLR   76 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCC--------CCCeeEEEecCccchhhhhhcccccccCcceEE
Confidence            468999999999999999999999999999999875432        457999999999999999999999999999999


Q ss_pred             EEecCccccchhhh------------hhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCC
Q psy3345         659 LKRSNRNLESEATT------------VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL  726 (787)
Q Consensus       659 v~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~  726 (787)
                      |.++..........            ......+.......+|.|.+||+..+++||++.+.+-|.|....+.++      
T Consensus        77 VEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------  150 (241)
T KOG0105|consen   77 VEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------  150 (241)
T ss_pred             EEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------
Confidence            99987553210000            000011122335689999999999999999999999999999988887      


Q ss_pred             CceEEEEEecCHHHHHHHHHHhcC
Q psy3345         727 HRGFGFVEFITKNEAKRAMKALCQ  750 (787)
Q Consensus       727 ~~g~afV~F~~~~~A~~Al~~l~~  750 (787)
                        |.+.|+|...++.+=|+..|..
T Consensus       151 --g~GvV~~~r~eDMkYAvr~ld~  172 (241)
T KOG0105|consen  151 --GVGVVEYLRKEDMKYAVRKLDD  172 (241)
T ss_pred             --cceeeeeeehhhHHHHHHhhcc
Confidence              5899999999999999999974

>KOG0105|consensus

Probab=99.69  E-value=1.3e-15  Score=136.13  Aligned_cols=178  Identities=28%  Similarity=0.312  Sum_probs=139.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ...++|||+|||.++.+.+|.++|.+||.|.+|.+..-   ....+||||+|.++.+|..|+..-+|..+.|..|+|.++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            35679999999999999999999999999999988432   335679999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCC----CccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEE
Q psy3345         414 KPKENEGNVDG----KVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVE  489 (787)
Q Consensus       414 ~~~~~~~~~~~----~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~  489 (787)
                      ..........+    ..+...+..   .-..++...+...|+|.+||.+.+.+||++++.+-|.|+...+.+++ ++.|+
T Consensus        81 rggr~s~~~~G~y~gggrgGgg~g---g~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg-~GvV~  156 (241)
T KOG0105|consen   81 RGGRSSSDRRGSYSGGGRGGGGGG---GRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDG-VGVVE  156 (241)
T ss_pred             cCCCcccccccccCCCCCCCCCCC---cccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeeccc-ceeee
Confidence            76521111111    001000000   00123355678899999999999999999999999999998888776 89999


Q ss_pred             eCCHHHHHHHHHHhcCCeeC--CeeEEEEEe
Q psy3345         490 FLQKNQAKAAFNSLAYTKFK--EVPLYLEWA  518 (787)
Q Consensus       490 F~~~~~A~~A~~~l~~~~~~--g~~l~v~~~  518 (787)
                      |...++.+-|+.+|....+.  |-..++...
T Consensus       157 ~~r~eDMkYAvr~ld~~~~~seGe~~yirv~  187 (241)
T KOG0105|consen  157 YLRKEDMKYAVRKLDDQKFRSEGETAYIRVR  187 (241)
T ss_pred             eeehhhHHHHHHhhccccccCcCcEeeEEec
Confidence            99999999999999887765  555555544

>KOG4206|consensus

Probab=99.68  E-value=1.1e-15  Score=143.23  Aligned_cols=172  Identities=24%  Similarity=0.368  Sum_probs=143.0

Q ss_pred             CCeEEecCCCCCCCHHHHHH----HHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCe
Q psy3345         580 DTTLYIKNLNFNSTEDSIRR----HFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH  655 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~~----~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~  655 (787)
                      ..+|||.||+..+..++|+.    +|++||.|..|...+.        ...+|-|||.|.+.+.|..|+..|+|..+.|+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt--------~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK   80 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT--------PKMRGQAFVVFKETEAASAALRALQGFPFYGK   80 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC--------CCccCceEEEecChhHHHHHHHHhcCCcccCc
Confidence            34999999999999999888    9999999999998763        45899999999999999999999999999999


Q ss_pred             EEEEEecCccccchhhhh----------------------hh---------ccc-----cccCCCCCEEEEecCCccCcH
Q psy3345         656 QIELKRSNRNLESEATTV----------------------KR---------KSS-----NVAKQTGSKILVRNIPFQAKQ  699 (787)
Q Consensus       656 ~l~v~~~~~~~~~~~~~~----------------------~~---------~~~-----~~~~~~~~~l~V~nLp~~~t~  699 (787)
                      .+++.+++.+...-....                      ..         ...     .....+...+++.|||.+++.
T Consensus        81 ~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~  160 (221)
T KOG4206|consen   81 PMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESES  160 (221)
T ss_pred             hhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhH
Confidence            999999986543211100                      00         000     112346788999999999999


Q ss_pred             HHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       700 ~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      +.|..+|..|..-..++++..      ..+.|||+|.+...|.-|.+.+.+.++-....|.+.||+
T Consensus       161 e~l~~lf~qf~g~keir~i~~------~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  161 EMLSDLFEQFPGFKEIRLIPP------RSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHHHHhhCcccceeEeccC------CCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999999999999876      368999999999999999999986555558999999986

>KOG4205|consensus

Probab=99.68  E-value=1.3e-16  Score=162.13  Aligned_cols=173  Identities=24%  Similarity=0.394  Sum_probs=150.7

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .+-+++|-+     |+|.+|++.|+++|+.||+|.+|.+++++ .|++|||+||+|++++...++|.. ..+.|+||.|+
T Consensus         5 ~~~KlfiGg-----isw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve   78 (311)
T KOG4205|consen    5 ESGKLFIGG-----LSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVE   78 (311)
T ss_pred             CCcceeecC-----cCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCcccc
Confidence            567899999     99999999999999999999999999999 799999999999999999999987 78899999999


Q ss_pred             EEEccCCCCCCCCCCcccCCCCChhHHhhcccCCCCCCCCCCcCCCCCCCCCCCCcchHHHHHHhCCCcccCccCCCCCC
Q psy3345          90 VEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVSKLLPLSNKDG  169 (787)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (787)
                      +..|.+..+...+                                                                   
T Consensus        79 ~k~av~r~~~~~~-------------------------------------------------------------------   91 (311)
T KOG4205|consen   79 PKRAVSREDQTKV-------------------------------------------------------------------   91 (311)
T ss_pred             ceeccCccccccc-------------------------------------------------------------------
Confidence            9888760000000                                                                   


Q ss_pred             CccccccccccccccccCCCCcHHHHhhccCCCCCCCCCCCCCCCCCCCcCCCccceEEEeCCCCCCCHHhHHHhhcCCC
Q psy3345         170 EEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLP  249 (787)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~te~di~~~F~~~g  249 (787)
                                                                         .                            
T Consensus        92 ---------------------------------------------------~----------------------------   92 (311)
T KOG4205|consen   92 ---------------------------------------------------G----------------------------   92 (311)
T ss_pred             ---------------------------------------------------c----------------------------
Confidence                                                               0                            


Q ss_pred             CcceeecccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecccCCccccCCCcCCCCchhhhhhhhcccccccchhhh
Q psy3345         250 LASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQF  329 (787)
Q Consensus       250 ~v~i~i~~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  329 (787)
                                                                                                      
T Consensus        93 --------------------------------------------------------------------------------   92 (311)
T KOG4205|consen   93 --------------------------------------------------------------------------------   92 (311)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             hcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q psy3345         330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH  409 (787)
Q Consensus       330 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~  409 (787)
                        .......|||++||.++++++++++|.+||.|..+.++.|..+.+++||+||.|.+.+...+++. ...+.|+|+.+.
T Consensus        93 --~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~ve  169 (311)
T KOG4205|consen   93 --RHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVE  169 (311)
T ss_pred             --cccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceee
Confidence              00012269999999999999999999999999999999999999999999999999999999986 678899999999


Q ss_pred             EeeCCCCCC
Q psy3345         410 LIPGKPKEN  418 (787)
Q Consensus       410 v~~~~~~~~  418 (787)
                      |..+.+++.
T Consensus       170 vkrA~pk~~  178 (311)
T KOG4205|consen  170 VKRAIPKEV  178 (311)
T ss_pred             Eeeccchhh
Confidence            999998844

>KOG4206|consensus

Probab=99.62  E-value=1.5e-14  Score=135.75  Aligned_cols=198  Identities=18%  Similarity=0.245  Sum_probs=141.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHH----hhccCCCeeEEEecC---CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEec
Q psy3345         447 KRIILVKNLPYRTLPTDLKA----LFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  519 (787)
Q Consensus       447 ~~~i~v~nlp~~~t~~~l~~----~F~~~G~v~~v~i~~---~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  519 (787)
                      ..+|||.||+..+..++|+.    +|++||.|..|....   -+|.|||.|.+.+.|-.|+..|+|..|+|+++.++||.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            44999999999999999887    999999999888764   55799999999999999999999999999999999996


Q ss_pred             Ccc--ccccccccccccccccccccccchhhhhcccccccccCCCcccccccccc----cccCCCCCCeEEecCCCCCCC
Q psy3345         520 EGV--FAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEED----EEREPEPDTTLYIKNLNFNST  593 (787)
Q Consensus       520 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~l~V~NLp~~~t  593 (787)
                      .+.  +........... +....+..        ....+..+.......+.....    ......+...+++.|||..++
T Consensus        89 s~sdii~~~~~~~v~~~-~k~~~~~~--------~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~  159 (221)
T KOG4206|consen   89 SDSDIIAQAPGTFVEKE-KKINGEIL--------ARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESE  159 (221)
T ss_pred             CccchhhccCceecccc-Cccccccc--------cccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchh
Confidence            652  211111000000 00000000        000000000000000000000    122356678999999999999


Q ss_pred             HHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC-CeEEEEEecC
Q psy3345         594 EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD-EHQIELKRSN  663 (787)
Q Consensus       594 ~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~-g~~l~v~~~~  663 (787)
                      .+.+..+|.+|+....++++...          .|.|||+|.+...|..|...++|..+. .+.+.|.++.
T Consensus       160 ~e~l~~lf~qf~g~keir~i~~~----------~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  160 SEMLSDLFEQFPGFKEIRLIPPR----------SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHHHHHhhCcccceeEeccCC----------CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999999999999988643          389999999999999999999999887 8888888764

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.62  E-value=3.6e-15  Score=136.92  Aligned_cols=82  Identities=18%  Similarity=0.350  Sum_probs=77.9

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ...+++|+|.|     ||+++||++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|+.||+.||+..|+|+.
T Consensus        31 ~~~~~~lfVgn-----L~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~  105 (144)
T PLN03134         31 RLMSTKLFIGG-----LSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRH  105 (144)
T ss_pred             cCCCCEEEEeC-----CCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            45677899999     99999999999999999999999999988 7999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.++.+
T Consensus       106 l~V~~a~~  113 (144)
T PLN03134        106 IRVNPAND  113 (144)
T ss_pred             EEEEeCCc
Confidence            99999986

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.61  E-value=3.7e-15  Score=136.88  Aligned_cols=86  Identities=21%  Similarity=0.448  Sum_probs=79.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||.|||+.+|+++|+++|++||.|.+++|+.+. .+++++|||||+|.+.++|+.|+..|| +..+.|++|+|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~kGfaFV~F~~~e~A~~Al~~ln-g~~i~Gr~l~V  108 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDR-ETGRSRGFGFVNFNDEGAATAAISEMD-GKELNGRHIRV  108 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecC-CCCCcceEEEEEECCHHHHHHHHHHcC-CCEECCEEEEE
Confidence            4567899999999999999999999999999999999886 689999999999999999999999997 69999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus       109 ~~a~~~~~  116 (144)
T PLN03134        109 NPANDRPS  116 (144)
T ss_pred             EeCCcCCC
Confidence            99986554

>KOG1548|consensus

Probab=99.55  E-value=1.8e-13  Score=135.01  Aligned_cols=177  Identities=20%  Similarity=0.401  Sum_probs=137.8

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEE--------EEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS--------VTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQ  648 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~--------v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~ln  648 (787)
                      ....+.|||.|||.++|.+++.++|++||.|..        |+|.++..      |..+|-|.++|-..++..-|+..|+
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~------G~lKGDaLc~y~K~ESVeLA~~ilD  204 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ------GKLKGDALCCYIKRESVELAIKILD  204 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC------CCccCceEEEeecccHHHHHHHHhC
Confidence            344567999999999999999999999998754        67776654      7899999999999999999999999


Q ss_pred             CCccCCeEEEEEecCccccc---------------hhhhhhhcc---------ccccCCCCCEEEEecC--C--ccCc--
Q psy3345         649 NSSLDEHQIELKRSNRNLES---------------EATTVKRKS---------SNVAKQTGSKILVRNI--P--FQAK--  698 (787)
Q Consensus       649 g~~l~g~~l~v~~~~~~~~~---------------~~~~~~~~~---------~~~~~~~~~~l~V~nL--p--~~~t--  698 (787)
                      +..+.|+.|+|..+.-....               ......+..         ........++|.++|+  |  +..+  
T Consensus       205 e~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~  284 (382)
T KOG1548|consen  205 EDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPD  284 (382)
T ss_pred             cccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHH
Confidence            99999999999887522111               000011100         1122235688999999  2  2223  


Q ss_pred             -----HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         699 -----QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       699 -----~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                           .+||++-+++||.|.+|.|.-..     +.|.+-|.|.+.++|..+++.|+ |++|.||.|..+.-.
T Consensus       285 l~~dlkedl~eec~K~G~v~~vvv~d~h-----PdGvvtV~f~n~eeA~~ciq~m~-GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  285 LLNDLKEDLTEECEKFGQVRKVVVYDRH-----PDGVVTVSFRNNEEADQCIQTMD-GRWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHHHHHHHHHhCCcceEEEeccC-----CCceeEEEeCChHHHHHHHHHhc-CeeecceEEEEEEeC
Confidence                 46688889999999999886543     67899999999999999999996 899999999876543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.50  E-value=9.4e-14  Score=111.81  Aligned_cols=70  Identities=26%  Similarity=0.463  Sum_probs=64.2

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      |+|.|     ||+++|++||+++|+.||.|.+|++..+++|+++|+|||.|.++++|.+|++.+++..|+||+|+
T Consensus         1 v~i~n-----lp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISN-----LPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEES-----STTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeC-----CCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            45666     99999999999999999999999999998899999999999999999999999998999999985

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0106|consensus

Probab=99.50  E-value=4.3e-14  Score=134.48  Aligned_cols=166  Identities=25%  Similarity=0.483  Sum_probs=135.6

Q ss_pred             CeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Q psy3345         581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK  660 (787)
Q Consensus       581 ~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~  660 (787)
                      ..+||++||+.+.+.+|..+|..||.+..+.+..             ||+||+|.+.-+|..|+..+|+..|.|..+.|.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-------------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve   68 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN-------------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVE   68 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec-------------ccceeccCchhhhhcccchhcCceecceeeeee
Confidence            4689999999999999999999999999887763             899999999999999999999999999988888


Q ss_pred             ecCccccchhhhh--h----hccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEE
Q psy3345         661 RSNRNLESEATTV--K----RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE  734 (787)
Q Consensus       661 ~~~~~~~~~~~~~--~----~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~  734 (787)
                      ++...........  .    ......+....+.+.|.|++..+.+++|.+.|+.+|.+....+         +++++||+
T Consensus        69 ~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---------~~~~~~v~  139 (216)
T KOG0106|consen   69 HARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---------RRNFAFVE  139 (216)
T ss_pred             cccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---------hcccccee
Confidence            8764322110000  0    1111223456789999999999999999999999999955544         35689999


Q ss_pred             ecCHHHHHHHHHHhcCCeeecCceEEEEEcccccc
Q psy3345         735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       735 F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~  769 (787)
                      |.+.++|.+|+..|+ +..+.|++|.+..+-.+..
T Consensus       140 Fs~~~da~ra~~~l~-~~~~~~~~l~~~~~~~d~~  173 (216)
T KOG0106|consen  140 FSEQEDAKRALEKLD-GKKLNGRRISVEKNSRDRS  173 (216)
T ss_pred             ehhhhhhhhcchhcc-chhhcCceeeecccCcchh
Confidence            999999999999997 7999999999966654443

>PF00076 RRM_1: RNA recognition motif

Probab=99.49  E-value=1.2e-13  Score=111.32  Aligned_cols=70  Identities=21%  Similarity=0.459  Sum_probs=66.2

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      |+|.|     ||+++|+++|+++|+.||.|..+.+..+..|+++|+|||.|.+.++|.+|++.||+..++|+.|+
T Consensus         1 l~v~n-----lp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGN-----LPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEES-----ETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcC-----CCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            45666     99999999999999999999999999988899999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG4207|consensus

Probab=99.48  E-value=2.6e-14  Score=130.44  Aligned_cols=77  Identities=25%  Similarity=0.440  Sum_probs=73.3

Q ss_pred             cCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEccC
Q psy3345          19 DLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        19 ~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~~   95 (787)
                      -|+|.||.|-+|.++|+.+|.+||.|-||.|+.++ ++.++|||||.|....||+.|++.|||..++||-|.|.+|+=
T Consensus        15 SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   15 SLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             eEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            35667799999999999999999999999999999 899999999999999999999999999999999999999984

>KOG0122|consensus

Probab=99.47  E-value=8.9e-14  Score=130.79  Aligned_cols=76  Identities=21%  Similarity=0.307  Sum_probs=73.3

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEc
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      |.|.|     ||-+++|+||++||..||.|..|.|.+++ +|.++|||||.|.+.+||++||..|||.=+++-.|.|+++
T Consensus       192 vRvtN-----Lsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  192 VRVTN-----LSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             eEEec-----CccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            66666     99999999999999999999999999999 8999999999999999999999999999999999999999


Q ss_pred             cC
Q psy3345          94 SN   95 (787)
Q Consensus        94 ~~   95 (787)
                      +|
T Consensus       267 kP  268 (270)
T KOG0122|consen  267 KP  268 (270)
T ss_pred             CC
Confidence            97

>KOG1548|consensus

Probab=99.47  E-value=9.6e-13  Score=129.91  Aligned_cols=182  Identities=23%  Similarity=0.293  Sum_probs=139.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR  406 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~  406 (787)
                      -+..|||.|||.++|.+++.++|++||.|..        |.+.++.. |..+|-|.+.|-..++..-|++.|++..+.|+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            3557999999999999999999999997764        77777754 99999999999999999999999999999999


Q ss_pred             EEEEeeCCCCCCCC-CCCCCcc-ccccccc------------cchhhhhhhcCCCCEEEEeCCCCC----CC-------H
Q psy3345         407 MLHLIPGKPKENEG-NVDGKVH-CCISERK------------LDAFNQVVEARSKRIILVKNLPYR----TL-------P  461 (787)
Q Consensus       407 ~l~v~~~~~~~~~~-~~~~~~~-~a~~~~~------------~~~~~~~~~~~~~~~i~v~nlp~~----~t-------~  461 (787)
                      .|+|..+.-..... ....... .+..-..            .+. ..+...+..++|+++|+-..    .+       .
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~-~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDR-DDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCc-cccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            99999886541110 0000000 0000000            000 12334556789999998432    23       4


Q ss_pred             HHHHHhhccCCCeeEEEec--CCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEe
Q psy3345         462 TDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  518 (787)
Q Consensus       462 ~~l~~~F~~~G~v~~v~i~--~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~  518 (787)
                      ++|.+.+++||.|.+|.+.  +..|.+.|.|.+.++|..|++.|+|+.|.||.|..+..
T Consensus       291 edl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~  349 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIW  349 (382)
T ss_pred             HHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEe
Confidence            6777889999999999987  46689999999999999999999999999999988765

>KOG1457|consensus

Probab=99.45  E-value=1e-12  Score=121.45  Aligned_cols=195  Identities=22%  Similarity=0.298  Sum_probs=125.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC--CC-----cEEEEEeCCHHHHHHHHHHhcCCeeC---CeeEEE
Q psy3345         446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YG-----ITGLVEFLQKNQAKAAFNSLAYTKFK---EVPLYL  515 (787)
Q Consensus       446 ~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~--~~-----~~a~V~F~~~~~A~~A~~~l~~~~~~---g~~l~v  515 (787)
                      .-++|||.+||.++...+|..+|..|-.-+...+..  .+     -+|||.|.+..+|..|+..|||..|.   +..|.+
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            368999999999999999999999986665444432  22     47999999999999999999999997   789999


Q ss_pred             EEecCccccccccccccccccccccccc--cchhhhh----cc-------------------------ccccc---ccCC
Q psy3345         516 EWAPEGVFAEAKEKSKGKEKEKNEEEGE--EGEEEKK----EN-------------------------TAEED---NQQG  561 (787)
Q Consensus       516 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~----~~-------------------------~~~~~---~~~~  561 (787)
                      +++..+.-........   .+.......  ......+    ..                         +..+.   .++.
T Consensus       113 ElAKSNtK~kr~k~sg---tP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~  189 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSG---TPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSK  189 (284)
T ss_pred             eehhcCcccccCCCCC---CCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhc
Confidence            9987652111111000   000000000  0000000    00                         00000   0000


Q ss_pred             Cccccc--ccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHH
Q psy3345         562 VPEVEE--NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES  639 (787)
Q Consensus       562 ~~~~~~--~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~  639 (787)
                      -++...  ....+.......-.+|||-||.+++|+++|+.+|+.|......+|...         ..+..||++|.+.+.
T Consensus       190 ~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~---------~g~~vaf~~~~~~~~  260 (284)
T KOG1457|consen  190 APSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR---------GGMPVAFADFEEIEQ  260 (284)
T ss_pred             CCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC---------CCcceEeecHHHHHH
Confidence            011100  000011111122348999999999999999999999998887777532         246789999999999


Q ss_pred             HHHHHHHhCCCcc
Q psy3345         640 LNQALKVLQNSSL  652 (787)
Q Consensus       640 A~~A~~~lng~~l  652 (787)
                      |..|+..|+|..|
T Consensus       261 at~am~~lqg~~~  273 (284)
T KOG1457|consen  261 ATDAMNHLQGNLL  273 (284)
T ss_pred             HHHHHHHhhccee
Confidence            9999999999876

>PF00076 RRM_1: RNA recognition motif

Probab=99.45  E-value=4.5e-13  Score=107.87  Aligned_cols=70  Identities=31%  Similarity=0.600  Sum_probs=67.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q psy3345         339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH  409 (787)
Q Consensus       339 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~  409 (787)
                      |||+|||.++|+++|+++|+.||.|..+.+..+ .++..+|+|||+|.+.++|.+|++.|+|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999987 6788999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0121|consensus

Probab=99.43  E-value=2.8e-13  Score=114.11  Aligned_cols=84  Identities=26%  Similarity=0.459  Sum_probs=79.5

Q ss_pred             cccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       331 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      .....+++|||+||++.++|++|.++|+.+|+|..|.|-.|+.+..+.|||||+|-+.++|..|++-++|+.+..++|.+
T Consensus        31 ~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~  110 (153)
T KOG0121|consen   31 EALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRI  110 (153)
T ss_pred             HHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceee
Confidence            45567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy3345         411 IPGK  414 (787)
Q Consensus       411 ~~~~  414 (787)
                      .|..
T Consensus       111 D~D~  114 (153)
T KOG0121|consen  111 DWDA  114 (153)
T ss_pred             eccc
Confidence            8854

>KOG1457|consensus

Probab=99.42  E-value=2.1e-12  Score=119.43  Aligned_cols=176  Identities=21%  Similarity=0.288  Sum_probs=126.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCC-CCcceEEEEEEcCHHHHHHHHHHhCCceeC---CeEEE
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET-DKTKGFALVTFLMPEHATQAYQHLDGTVFL---GRMLH  409 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~-~~~~g~afV~F~~~~~A~~a~~~l~~~~~~---g~~l~  409 (787)
                      ...++|||.+||.++...+|+.+|..|-......+...... .-.+-+||+.|.+..+|..|+..|||..|+   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            44689999999999999999999999866666666433222 225579999999999999999999999884   68999


Q ss_pred             EeeCCCCCCCCCCC-----C-Cc-----------c-----------------------ccccc-----------------
Q psy3345         410 LIPGKPKENEGNVD-----G-KV-----------H-----------------------CCISE-----------------  432 (787)
Q Consensus       410 v~~~~~~~~~~~~~-----~-~~-----------~-----------------------~a~~~-----------------  432 (787)
                      |..++...+.....     + +.           +                       .++.+                 
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            98876541110000     0 00           0                       00000                 


Q ss_pred             ---cccchhh-hhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCc--EEEEEeCCHHHHHHHHHHhcCC
Q psy3345         433 ---RKLDAFN-QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI--TGLVEFLQKNQAKAAFNSLAYT  506 (787)
Q Consensus       433 ---~~~~~~~-~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~--~a~V~F~~~~~A~~A~~~l~~~  506 (787)
                         ..+..-+ .....+.-.++||.||...+++++|+.+|+.|.....++|...+|  .||++|.+.+.|..|+..|+|.
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~  271 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGN  271 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcc
Confidence               0000000 001112236799999999999999999999999888888876555  6999999999999999999987


Q ss_pred             eeC
Q psy3345         507 KFK  509 (787)
Q Consensus       507 ~~~  509 (787)
                      .+.
T Consensus       272 ~~s  274 (284)
T KOG1457|consen  272 LLS  274 (284)
T ss_pred             eec
Confidence            654

>KOG0106|consensus

Probab=99.41  E-value=5.2e-13  Score=127.15  Aligned_cols=166  Identities=26%  Similarity=0.379  Sum_probs=133.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      ..+||++||+.+.+.+|..+|..||.+.++.+.        .||+||+|.+..+|..|+..+++..|.|-.+.|.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            369999999999999999999999999998873        258999999999999999999999999988888888753


Q ss_pred             CCCCCCC-CCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHH
Q psy3345         417 ENEGNVD-GKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQ  495 (787)
Q Consensus       417 ~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~  495 (787)
                      ....... +..+.+.      .-...........++|.|++..+...+|.+.|..+|.+....+  ..+.+||+|.+.++
T Consensus        74 ~~~~g~~~~g~r~~~------~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~d  145 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSD------SRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQED  145 (216)
T ss_pred             ccccCCCCCCCccch------hhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhh
Confidence            1111000 0001110      0112234556889999999999999999999999999954444  56789999999999


Q ss_pred             HHHHHHHhcCCeeCCeeEEEEEe
Q psy3345         496 AKAAFNSLAYTKFKEVPLYLEWA  518 (787)
Q Consensus       496 A~~A~~~l~~~~~~g~~l~v~~~  518 (787)
                      |.+|+..|++..+.++.|.+...
T Consensus       146 a~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  146 AKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             hhhcchhccchhhcCceeeeccc
Confidence            99999999999999999999444

>KOG0125|consensus

Probab=99.40  E-value=6.3e-13  Score=130.13  Aligned_cols=77  Identities=21%  Similarity=0.384  Sum_probs=72.3

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      .||.|.|     +||..-|.||+..|.+||.|.||.|+.+. ..|+|||||+|++++||.+|-.+|||+.|.||+|+|-.
T Consensus        97 kRLhVSN-----IPFrFRdpDL~aMF~kfG~VldVEIIfNE-RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   97 KRLHVSN-----IPFRFRDPDLRAMFEKFGKVLDVEIIFNE-RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             ceeEeec-----CCccccCccHHHHHHhhCceeeEEEEecc-CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            4577777     99999999999999999999999999984 45899999999999999999999999999999999999


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      |++
T Consensus       171 ATa  173 (376)
T KOG0125|consen  171 ATA  173 (376)
T ss_pred             cch
Confidence            987

>KOG0122|consensus

Probab=99.40  E-value=9.5e-13  Score=123.94  Aligned_cols=82  Identities=39%  Similarity=0.582  Sum_probs=79.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      +.++|.|.|||.+++|.+|+++|.+||.|..+.+.+|+.||.++|||||.|.+.++|.+||..|||.-+..-.|+|.|+.
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            67789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy3345         415 PK  416 (787)
Q Consensus       415 ~~  416 (787)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.39  E-value=1.7e-12  Score=127.02  Aligned_cols=77  Identities=13%  Similarity=0.287  Sum_probs=71.2

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      ...|+|.|     ||+.+||+||++||+.||.|.+|.|+.++  .++|||||+|.++++|..||. |||..|.||.|.|.
T Consensus         4 ~rtVfVgN-----Ls~~tTE~dLrefFS~~G~I~~V~I~~d~--~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt   75 (260)
T PLN03120          4 VRTVKVSN-----VSLKATERDIKEFFSFSGDIEYVEMQSEN--ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTIT   75 (260)
T ss_pred             CCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEeecC--CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEE
Confidence            56789999     99999999999999999999999999874  467999999999999999996 79999999999999


Q ss_pred             EccCC
Q psy3345          92 KCSNL   96 (787)
Q Consensus        92 ~~~~~   96 (787)
                      ++...
T Consensus        76 ~a~~~   80 (260)
T PLN03120         76 PAEDY   80 (260)
T ss_pred             eccCC
Confidence            99864

>KOG0125|consensus

Probab=99.38  E-value=9.9e-13  Score=128.77  Aligned_cols=82  Identities=30%  Similarity=0.532  Sum_probs=75.4

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|+|.|||+...+-||+.+|.+||.|.+|.|+.+  +.| +||||||+|.++++|.+|-.+|+ |+++.||+|.|
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERG-SKGFGFVTmen~~dadRARa~LH-gt~VEGRkIEV  168 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERG-SKGFGFVTMENPADADRARAELH-GTVVEGRKIEV  168 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCC-CCccceEEecChhhHHHHHHHhh-cceeeceEEEE
Confidence            345689999999999999999999999999999999988  455 79999999999999999999995 89999999999


Q ss_pred             EEcccc
Q psy3345         762 EWAEEA  767 (787)
Q Consensus       762 ~~A~~~  767 (787)
                      .-|.+.
T Consensus       169 n~ATar  174 (376)
T KOG0125|consen  169 NNATAR  174 (376)
T ss_pred             eccchh
Confidence            999854

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.37  E-value=3.1e-12  Score=102.88  Aligned_cols=70  Identities=36%  Similarity=0.673  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q psy3345         339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH  409 (787)
Q Consensus       339 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~  409 (787)
                      |||+|||+++++++|+++|+.||.|..+.+..++. +.++|+|||+|.+.++|.+|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 89999999999999999999999998999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0114|consensus

Probab=99.36  E-value=5.4e-12  Score=102.21  Aligned_cols=92  Identities=24%  Similarity=0.431  Sum_probs=78.6

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....+-|||+|||+.+|.++..++|.+||.|..|+|--.    ...+|.|||.|.+..+|.+|+..|+ |..+.++.|+|
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~----k~TrGTAFVVYedi~dAk~A~dhls-g~n~~~ryl~v   89 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT----KETRGTAFVVYEDIFDAKKACDHLS-GYNVDNRYLVV   89 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc----cCcCceEEEEehHhhhHHHHHHHhc-ccccCCceEEE
Confidence            345678999999999999999999999999999998443    3468999999999999999999997 89999999999


Q ss_pred             EEccccccHHHHHHHHh
Q psy3345         762 EWAEEADNVEDIRKRTN  778 (787)
Q Consensus       762 ~~A~~~~~~~~~~~~~~  778 (787)
                      -|-.+.+....+..+.+
T Consensus        90 lyyq~~~~~~~~~~~k~  106 (124)
T KOG0114|consen   90 LYYQPEDAFKLMDSRKA  106 (124)
T ss_pred             EecCHHHHHHHHHhHHh
Confidence            99988776544444433

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.35  E-value=3.3e-12  Score=125.05  Aligned_cols=75  Identities=19%  Similarity=0.378  Sum_probs=69.6

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      .++|||+|||+.+|+++|+++|+.||.|.+|+|+.+.    .++|||||+|.++++|..||. || |..|.|++|.|+++
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~----~~~GfAFVtF~d~eaAe~All-Ln-G~~l~gr~V~Vt~a   77 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN----ERSQIAYVTFKDPQGAETALL-LS-GATIVDQSVTITPA   77 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC----CCCCEEEEEeCcHHHHHHHHH-hc-CCeeCCceEEEEec
Confidence            5789999999999999999999999999999998873    357999999999999999995 86 79999999999999


Q ss_pred             c
Q psy3345         765 E  765 (787)
Q Consensus       765 ~  765 (787)
                      .
T Consensus        78 ~   78 (260)
T PLN03120         78 E   78 (260)
T ss_pred             c
Confidence            7

>KOG4207|consensus

Probab=99.35  E-value=1.2e-12  Score=119.74  Aligned_cols=81  Identities=26%  Similarity=0.491  Sum_probs=77.2

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...+.|.|-||-+.++.++|+.+|++||.|-+|.|+.+. -+++++|||||.|....+|+.|+.+|+ |..|+|+.|.|+
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr-~Tr~sRgFaFVrf~~k~daedA~damD-G~~ldgRelrVq   88 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDR-YTRQSRGFAFVRFHDKRDAEDALDAMD-GAVLDGRELRVQ   88 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceeccccc-ccccccceeEEEeeecchHHHHHHhhc-ceeeccceeeeh
Confidence            356889999999999999999999999999999999997 689999999999999999999999998 799999999999


Q ss_pred             Ecc
Q psy3345         763 WAE  765 (787)
Q Consensus       763 ~A~  765 (787)
                      +|.
T Consensus        89 ~ar   91 (256)
T KOG4207|consen   89 MAR   91 (256)
T ss_pred             hhh
Confidence            997

>KOG0149|consensus

Probab=99.33  E-value=1.6e-12  Score=122.25  Aligned_cols=79  Identities=27%  Similarity=0.437  Sum_probs=74.3

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      .-++|||.||+++++.+.|+++|++||+|..+.|+.|+ .+|+++|||||+|.+.++|.+|++.-|  ..++||+-.+.+
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~-~t~rskGyGfVTf~d~~aa~rAc~dp~--piIdGR~aNcnl   87 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDK-NTGRSKGYGFVTFRDAEAATRACKDPN--PIIDGRKANCNL   87 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEecc-CCccccceeeEEeecHHHHHHHhcCCC--Ccccccccccch
Confidence            45789999999999999999999999999999999997 799999999999999999999999875  799999999998


Q ss_pred             cc
Q psy3345         764 AE  765 (787)
Q Consensus       764 A~  765 (787)
                      |.
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            86

>KOG0149|consensus

Probab=99.32  E-value=2.2e-12  Score=121.30  Aligned_cols=78  Identities=15%  Similarity=0.268  Sum_probs=73.5

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      -++|+|-|     |||.++.++|+++|..||+|.++.|+.|+ +|+|+|||||+|.+.+.|.+|.+. -+-.|+||+..+
T Consensus        12 ~TKifVgg-----L~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNc   85 (247)
T KOG0149|consen   12 FTKIFVGG-----LAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANC   85 (247)
T ss_pred             EEEEEEcC-----cccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCccccccccc
Confidence            36899999     99999999999999999999999999999 899999999999999999999998 678999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      -+|.-
T Consensus        86 nlA~l   90 (247)
T KOG0149|consen   86 NLASL   90 (247)
T ss_pred             chhhh
Confidence            98874

>KOG0107|consensus

Probab=99.31  E-value=3.7e-12  Score=113.88  Aligned_cols=77  Identities=29%  Similarity=0.505  Sum_probs=72.3

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      +-.++|||.||+..+++.||..+|..||.|.+|.|-.+      +.|||||+|.++.+|..|+..|+ |+.|+|.+|.|+
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn------PPGfAFVEFed~RDA~DAvr~LD-G~~~cG~r~rVE   80 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN------PPGFAFVEFEDPRDAEDAVRYLD-GKDICGSRIRVE   80 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec------CCCceEEeccCcccHHHHHhhcC-CccccCceEEEE
Confidence            34789999999999999999999999999999999887      47999999999999999999997 799999999999


Q ss_pred             Eccc
Q psy3345         763 WAEE  766 (787)
Q Consensus       763 ~A~~  766 (787)
                      +...
T Consensus        81 ~S~G   84 (195)
T KOG0107|consen   81 LSTG   84 (195)
T ss_pred             eecC
Confidence            9873

>KOG0121|consensus

Probab=99.31  E-value=4.4e-12  Score=106.98  Aligned_cols=82  Identities=28%  Similarity=0.574  Sum_probs=75.0

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      ....++|||+||++.+++++|.++|+.+|+|..+.+=.|..     +..+-|||||+|.+.++|..|++.+||..|+.++
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~-----kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~  107 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRF-----KKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRP  107 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccC-----CcCccceEEEEEecchhHHHHHHHhccCcccccc
Confidence            34578999999999999999999999999999988777665     5678899999999999999999999999999999


Q ss_pred             EEEEecC
Q psy3345         657 IELKRSN  663 (787)
Q Consensus       657 l~v~~~~  663 (787)
                      |.+.|..
T Consensus       108 ir~D~D~  114 (153)
T KOG0121|consen  108 IRIDWDA  114 (153)
T ss_pred             eeeeccc
Confidence            9999864

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.30  E-value=2.4e-11  Score=127.77  Aligned_cols=164  Identities=24%  Similarity=0.443  Sum_probs=126.3

Q ss_pred             CCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Q psy3345         580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIEL  659 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v  659 (787)
                      .++|||+|||+.+++++|.++|..||.|..+.+..+..     ++.++|||||+|.+.++|..|+..++|..+.|+.|.|
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~-----~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v  189 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRE-----TGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRV  189 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccc-----cCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEe
Confidence            69999999999999999999999999999999999864     6889999999999999999999999999999999999


Q ss_pred             EecCc--cccchhh----h----hhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCce
Q psy3345         660 KRSNR--NLESEAT----T----VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG  729 (787)
Q Consensus       660 ~~~~~--~~~~~~~----~----~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g  729 (787)
                      .+...  .......    .    ...............+++.|++..++..++...|..+|.+....+.... .......
T Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  268 (306)
T COG0724         190 QKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSK-DGKIPKS  268 (306)
T ss_pred             eccccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCC-CCccccc
Confidence            99642  1111000    0    0011122334577899999999999999999999999999777776653 2223344


Q ss_pred             EEEEEecCHHHHHHHHHHhc
Q psy3345         730 FGFVEFITKNEAKRAMKALC  749 (787)
Q Consensus       730 ~afV~F~~~~~A~~Al~~l~  749 (787)
                      +.++.+.....+..++....
T Consensus       269 ~~~~~~~~~~~~~~~~~~~~  288 (306)
T COG0724         269 RSFVGNEASKDALESNSRGN  288 (306)
T ss_pred             ccccchhHHHhhhhhhcccc
Confidence            44566665555555555443

>smart00360 RRM RNA recognition motif

Probab=99.29  E-value=1.1e-11  Score=99.62  Aligned_cols=69  Identities=28%  Similarity=0.453  Sum_probs=65.1

Q ss_pred             cCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          23 VEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        23 ~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      .|||+.+++++|+++|+.||.|..+.+..++ .++++|+|||.|.+.++|..|++.+|+..++|++|.|.
T Consensus         2 ~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        2 GNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            4599999999999999999999999999987 58999999999999999999999999999999999873

>KOG0111|consensus

Probab=99.28  E-value=2.5e-12  Score=118.53  Aligned_cols=84  Identities=26%  Similarity=0.515  Sum_probs=79.8

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||.+|..++|+.-|...|=+||.|.+|.+|.++ .++++||||||+|.-.++|..||..|| +..|+||.|+|.
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDy-esqkHRgFgFVefe~aEDAaaAiDNMn-esEL~GrtirVN   85 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDY-ESQKHRGFGFVEFEEAEDAAAAIDNMN-ESELFGRTIRVN   85 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccch-hcccccceeEEEeeccchhHHHhhcCc-hhhhcceeEEEe
Confidence            456889999999999999999999999999999999996 899999999999999999999999997 799999999999


Q ss_pred             Eccccc
Q psy3345         763 WAEEAD  768 (787)
Q Consensus       763 ~A~~~~  768 (787)
                      ||+|..
T Consensus        86 ~AkP~k   91 (298)
T KOG0111|consen   86 LAKPEK   91 (298)
T ss_pred             ecCCcc
Confidence            999865

>PLN03213 repressor of silencing 3; Provisional

Probab=99.28  E-value=1.2e-11  Score=126.96  Aligned_cols=79  Identities=22%  Similarity=0.401  Sum_probs=73.0

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCH--HHHHHHHHHhcCCeeecCceEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK--NEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~--~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ..+.+|||+||++.+|++||+.+|+.||.|.+|.|++.   +|  ||||||+|.+.  .++.+||..|| |..+.||.|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE---TG--RGFAFVEMssdddaEeeKAISaLN-GAEWKGR~LK   81 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT---KG--RSFAYIDFSPSSTNSLTKLFSTYN-GCVWKGGRLR   81 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc---cC--CceEEEEecCCcHHHHHHHHHHhc-CCeecCceeE
Confidence            45689999999999999999999999999999999954   67  99999999988  78999999997 7999999999


Q ss_pred             EEEcccc
Q psy3345         761 LEWAEEA  767 (787)
Q Consensus       761 v~~A~~~  767 (787)
                      |+-|+|.
T Consensus        82 VNKAKP~   88 (759)
T PLN03213         82 LEKAKEH   88 (759)
T ss_pred             EeeccHH
Confidence            9999854

>PLN03213 repressor of silencing 3; Provisional

Probab=99.27  E-value=1.1e-11  Score=127.25  Aligned_cols=76  Identities=21%  Similarity=0.355  Sum_probs=71.3

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCH--HHHHHHHHHhccCccCCceEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHRE--DQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~--~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ..+|+|.|     |+|.+|++||+.+|+.||.|.+|.|++. +|  ||||||.|.+.  .++.+||..|||..+.||.|+
T Consensus        10 gMRIYVGN-----LSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LK   81 (759)
T PLN03213         10 GVRLHVGG-----LGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLR   81 (759)
T ss_pred             ceEEEEeC-----CCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeE
Confidence            46899999     9999999999999999999999999943 56  99999999998  789999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |..|++
T Consensus        82 VNKAKP   87 (759)
T PLN03213         82 LEKAKE   87 (759)
T ss_pred             EeeccH
Confidence            999997

>KOG0126|consensus

Probab=99.27  E-value=6.8e-13  Score=118.88  Aligned_cols=83  Identities=30%  Similarity=0.514  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      .++.-|||+|||++.||.||.-+|++||.|++|.+++|+.||+++||||+.|.+..+..-|+..|||..|.||.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CCC
Q psy3345         414 KPK  416 (787)
Q Consensus       414 ~~~  416 (787)
                      ...
T Consensus       113 ~~Y  115 (219)
T KOG0126|consen  113 SNY  115 (219)
T ss_pred             ccc
Confidence            543

>smart00362 RRM_2 RNA recognition motif

Probab=99.26  E-value=2.4e-11  Score=98.02  Aligned_cols=71  Identities=28%  Similarity=0.472  Sum_probs=66.6

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      |+|.|     ||+.+++++|+++|..||.|..+.+..++ |.++|+|||.|.+.++|++|++.+++..+.|+.|.|.
T Consensus         2 v~i~~-----l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        2 LFVGN-----LPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             EEEcC-----CCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            66777     99999999999999999999999999887 8899999999999999999999999999999999873

>KOG0114|consensus

Probab=99.25  E-value=3.3e-11  Score=97.74  Aligned_cols=81  Identities=25%  Similarity=0.376  Sum_probs=73.1

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      +.-.+.|||+|||+++|.++..++|..||.|..++|=..+        ..+|.|||.|.+..+|.+|+..|+|..+.++.
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--------~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ry   86 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--------ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRY   86 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--------CcCceEEEEehHhhhHHHHHHHhcccccCCce
Confidence            3446789999999999999999999999999999996544        47899999999999999999999999999999


Q ss_pred             EEEEecCcc
Q psy3345         657 IELKRSNRN  665 (787)
Q Consensus       657 l~v~~~~~~  665 (787)
                      |.|-+....
T Consensus        87 l~vlyyq~~   95 (124)
T KOG0114|consen   87 LVVLYYQPE   95 (124)
T ss_pred             EEEEecCHH
Confidence            999887643

>KOG0130|consensus

Probab=99.24  E-value=1e-11  Score=105.57  Aligned_cols=83  Identities=30%  Similarity=0.439  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      -.+..|||.++...+||++|.+.|..||+|..+++-.|..||..+|||.|+|.+.++|+.|+..+||..+.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy3345         414 KPK  416 (787)
Q Consensus       414 ~~~  416 (787)
                      .-+
T Consensus       150 Fv~  152 (170)
T KOG0130|consen  150 FVK  152 (170)
T ss_pred             Eec
Confidence            754

>KOG0130|consensus

Probab=99.24  E-value=1.7e-11  Score=104.19  Aligned_cols=89  Identities=22%  Similarity=0.374  Sum_probs=80.9

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +|...-|+|.|     +...+||+||.+.|..||+|++++|-.++ +|-.+|||.|.|++.++|+.|+..+|+..+-|..
T Consensus        69 SVEGwIi~Vtg-----vHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~  143 (170)
T KOG0130|consen   69 SVEGWIIFVTG-----VHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQN  143 (170)
T ss_pred             ceeeEEEEEec-----cCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCc
Confidence            34556689999     99999999999999999999999999988 8999999999999999999999999999999999


Q ss_pred             EEEEEccCCCCCCCC
Q psy3345          88 IKVEKCSNLGDTTKP  102 (787)
Q Consensus        88 i~v~~~~~~~~~~~~  102 (787)
                      |.|.+|...+.+..+
T Consensus       144 v~VDw~Fv~gp~~g~  158 (170)
T KOG0130|consen  144 VSVDWCFVKGPERGK  158 (170)
T ss_pred             eeEEEEEecCCccCc
Confidence            999999975554443

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.23  E-value=4.2e-11  Score=115.14  Aligned_cols=75  Identities=12%  Similarity=0.273  Sum_probs=68.9

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      ..|+|.|     |++.+||+||++||+.||.|.+|+|+.+  ++..|||||+|.++++|..|+. |||..|.++.|.|..
T Consensus         6 ~TV~V~N-----LS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~   77 (243)
T PLN03121          6 YTAEVTN-----LSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITR   77 (243)
T ss_pred             eEEEEec-----CCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEe
Confidence            4578888     9999999999999999999999999987  6677999999999999999994 699999999999988


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      +..
T Consensus        78 ~~~   80 (243)
T PLN03121         78 WGQ   80 (243)
T ss_pred             Ccc
Confidence            765

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.22  E-value=7e-11  Score=95.79  Aligned_cols=73  Identities=25%  Similarity=0.398  Sum_probs=68.6

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      |.|+|     ||+.+++++|+++|..+|.|..+.+..++.++.+|+|||.|.+.++|..|++.+++..+.|++|.|.+
T Consensus         2 i~i~~-----l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           2 LFVGN-----LPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             EEEeC-----CCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            66777     99999999999999999999999999988778899999999999999999999999999999999863

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>smart00361 RRM_1 RNA recognition motif

Probab=99.21  E-value=3.9e-11  Score=95.96  Aligned_cols=60  Identities=20%  Similarity=0.338  Sum_probs=55.4

Q ss_pred             HHHHHHHhh----ccCceEEEE-EEecC-C--CCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          31 QEQLKAKFE----EKGTVTDVQ-LKYTT-E--GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        31 ~~~l~~~f~----~~g~i~~~~-~~~~~-~--g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ++||+++|+    .||.|.+|. |++++ +  |+++|||||.|.+.++|.+|++.|||..++||.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            689999999    999999996 77665 4  899999999999999999999999999999999986

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.21  E-value=2.2e-10  Score=120.38  Aligned_cols=145  Identities=34%  Similarity=0.525  Sum_probs=113.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP  415 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  415 (787)
                      .++|||+|||+++|+++|.++|..||.+..+.+..++.+|.++|||||.|.+.++|..|+..++|..+.|+.|.|.+...
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            67999999999999999999999999999999999988899999999999999999999999999999999999999653


Q ss_pred             --CCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCC
Q psy3345         416 --KENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG  483 (787)
Q Consensus       416 --~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~  483 (787)
                        ........   .......................+++.+++..++..++...|..+|.+....+....
T Consensus       195 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (306)
T COG0724         195 ASQPRSELSN---NLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSK  261 (306)
T ss_pred             cccccccccc---ccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCC
Confidence              11110000   000000000000122234567889999999999999999999999999777766533

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.20  E-value=7.5e-11  Score=113.45  Aligned_cols=78  Identities=22%  Similarity=0.173  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      .+.+|||+||++.+|+++|+++|+.||+|.+|.|+++   +...|+|||+|.++++|..|+. |+|..|.++.|.|.+..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            4578999999999999999999999999999999987   3456899999999999999995 99999999999998866


Q ss_pred             CC
Q psy3345         415 PK  416 (787)
Q Consensus       415 ~~  416 (787)
                      ..
T Consensus        80 ~y   81 (243)
T PLN03121         80 QY   81 (243)
T ss_pred             cc
Confidence            43

>KOG0107|consensus

Probab=99.20  E-value=4.6e-11  Score=106.92  Aligned_cols=80  Identities=29%  Similarity=0.492  Sum_probs=73.2

Q ss_pred             CCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEE
Q psy3345         578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI  657 (787)
Q Consensus       578 ~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l  657 (787)
                      ...+.|||+||+..+++.+|...|..||.|.+|.|..++.          |||||+|.++-+|..|+..|+|..|.|..|
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPP----------GfAFVEFed~RDA~DAvr~LDG~~~cG~r~   77 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPP----------GFAFVEFEDPRDAEDAVRYLDGKDICGSRI   77 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCC----------CceEEeccCcccHHHHHhhcCCccccCceE
Confidence            3468999999999999999999999999999999998554          899999999999999999999999999999


Q ss_pred             EEEecCcccc
Q psy3345         658 ELKRSNRNLE  667 (787)
Q Consensus       658 ~v~~~~~~~~  667 (787)
                      .|.++.-...
T Consensus        78 rVE~S~G~~r   87 (195)
T KOG0107|consen   78 RVELSTGRPR   87 (195)
T ss_pred             EEEeecCCcc
Confidence            9999875433

>KOG0113|consensus

Probab=99.19  E-value=6.5e-11  Score=114.80  Aligned_cols=82  Identities=32%  Similarity=0.531  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      .+-++|||.-|+++++|..|+..|+.||+|..|+|+.++.||+++|||||+|....+...|.+..+|..|.|+.|.|..-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             CC
Q psy3345         414 KP  415 (787)
Q Consensus       414 ~~  415 (787)
                      ..
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            43

>smart00362 RRM_2 RNA recognition motif

Probab=99.17  E-value=1.9e-10  Score=92.72  Aligned_cols=71  Identities=46%  Similarity=0.746  Sum_probs=66.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      +|+|+|||..++.++|+++|..||++..+.+..++  +.++|+|||+|.+.++|..|++.+++..+.|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            58999999999999999999999999999998775  778899999999999999999999999999999886

>PF13893 RRM_5: RNA recognition motif

Probab=99.16  E-value=1.1e-10  Score=89.03  Aligned_cols=56  Identities=25%  Similarity=0.388  Sum_probs=51.5

Q ss_pred             HHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEc
Q psy3345          34 LKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        34 l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      |+++|+.||.|.+|.+..++    +|+|||+|.+.++|..|++.||+..+.|+.|+|.+|
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999998763    699999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0126|consensus

Probab=99.15  E-value=6.8e-12  Score=112.52  Aligned_cols=80  Identities=25%  Similarity=0.441  Sum_probs=75.5

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .+.-|+|.|     |||.+||.||--.||.||+|.+|.|++|+ +|+|+||||..|++.-....|+..|||..|.||.|+
T Consensus        34 dsA~Iyigg-----l~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtir  108 (219)
T KOG0126|consen   34 DSAYIYIGG-----LPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIR  108 (219)
T ss_pred             cceEEEECC-----CcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEE
Confidence            355699999     99999999999999999999999999999 899999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.-+..
T Consensus       109 VDHv~~  114 (219)
T KOG0126|consen  109 VDHVSN  114 (219)
T ss_pred             eeeccc
Confidence            987764

>KOG0108|consensus

Probab=99.15  E-value=1e-10  Score=124.66  Aligned_cols=87  Identities=30%  Similarity=0.567  Sum_probs=81.9

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      +.|||+|+|+++++++|.++|+..|.|.++++..|+ ++|+.+||||++|.+.++|.+|++.|| |..+.||+|+|.||.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~-~tG~~~G~~f~~~~~~~~~~~a~~~lN-g~~~~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDR-ETGKPKGFGFCEFTDEETAERAIRNLN-GAEFNGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccc-cCCCcCceeeEecCchhhHHHHHHhcC-CcccCCceEEeeccc
Confidence            889999999999999999999999999999999997 899999999999999999999999997 799999999999999


Q ss_pred             ccccHHHHH
Q psy3345         766 EADNVEDIR  774 (787)
Q Consensus       766 ~~~~~~~~~  774 (787)
                      .+.+.+..+
T Consensus        97 ~~~~~~~~~  105 (435)
T KOG0108|consen   97 NRKNAERSL  105 (435)
T ss_pred             ccchhHHHH
Confidence            777755544

>PF13893 RRM_5: RNA recognition motif

Probab=99.14  E-value=1.8e-10  Score=87.80  Aligned_cols=56  Identities=39%  Similarity=0.714  Sum_probs=50.9

Q ss_pred             HHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       702 L~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      |+++|++||.|.++.+..+.      +++|||+|.+.++|..|++.|| +..+.|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~------~~~a~V~f~~~~~A~~a~~~l~-~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK------RGFAFVEFASVEDAQKAIEQLN-GRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS------TTEEEEEESSHHHHHHHHHHHT-TSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhC-CCEECCcEEEEEEC
Confidence            68899999999999997771      6899999999999999999997 79999999999997

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0128|consensus

Probab=99.13  E-value=2.8e-13  Score=148.58  Aligned_cols=328  Identities=16%  Similarity=0.110  Sum_probs=228.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHH-HHHHhcCCeeE-EEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         335 ESGRIFVRNLSYTVTEDDLT-KLFEKYGPLAE-VILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~-~~F~~~G~i~~-v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ..++..|.|-+..-+...|. ..|+-++-... ...   +.......+||++-..++++..++..+.+......+|.+.-
T Consensus       478 md~~R~iWn~imty~~~~iag~Wle~~~lE~~~g~~---~~~R~~~R~ay~~~~~~~~~~ev~~~~~r~Ere~gtl~~~~  554 (881)
T KOG0128|consen  478 MDKAREIWNFIMTYGGGSIAGKWLEAINLEREYGDG---PSARKVLRKAYSQVVDPEDALEVLEFFRRFEREYGTLESFD  554 (881)
T ss_pred             hhhhhHhhhccccCCcchHHHHHHHHHhHHHHhCCc---hhHHHHHHHHHhcCcCchhHHHHHHHHHHHHhccccHHHHh
Confidence            34578889999988888888 56655432221 111   11122556899999999999999987776555444443322


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHH-HHHHhhccCCCeeEEEecCCC------cE
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPT-DLKALFEPFGDLGRVLVPPYG------IT  485 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~-~l~~~F~~~G~v~~v~i~~~~------~~  485 (787)
                      ..+....+      +            ............+.|+.+..... .....|..+|.|..|.++..+      .+
T Consensus       555 ~~~~~~~p------r------------~~~~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~  616 (881)
T KOG0128|consen  555 LCPEKVLP------R------------VYEAPLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQ  616 (881)
T ss_pred             hhHHhhcc------h------------hhhhhhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccch
Confidence            22110000      0            00011123334556665555444 567889999999999998733      26


Q ss_pred             EEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCccc
Q psy3345         486 GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV  565 (787)
Q Consensus       486 a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  565 (787)
                      +++.+.....++.|.. .++..+.++.+.+..++.......+..                                    
T Consensus       617 ~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~~~~~~~~kv------------------------------------  659 (881)
T KOG0128|consen  617 QQKVQSKHGSAESATV-PAGGALANRSAAVGLADAEEKEENFKV------------------------------------  659 (881)
T ss_pred             hhhhhccccchhhccc-ccccccCCccccCCCCCchhhhhccCc------------------------------------
Confidence            7888888888888755 455556666555554433210000000                                    


Q ss_pred             ccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHH
Q psy3345         566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALK  645 (787)
Q Consensus       566 ~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~  645 (787)
                             .........++|++||++.+.+++|...|..+|.+..+++....+     .+.-+|+|+|.|..+++|.+|+.
T Consensus       660 -------s~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n-----~~~~rG~~Y~~F~~~~~~~aaV~  727 (881)
T KOG0128|consen  660 -------SPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKN-----EKRFRGKAYVEFLKPEHAGAAVA  727 (881)
T ss_pred             -------CchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhh-----ccccccceeeEeecCCchhhhhh
Confidence                   001112346899999999999999999999999988888774333     46788999999999999999999


Q ss_pred             HhCCCccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCC
Q psy3345         646 VLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG  725 (787)
Q Consensus       646 ~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g  725 (787)
                      ...++.++                               ...|+|.|.|+..|.++|+.+|+.+|.+++++++..  ..|
T Consensus       728 f~d~~~~g-------------------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~--r~g  774 (881)
T KOG0128|consen  728 FRDSCFFG-------------------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV--RAG  774 (881)
T ss_pred             hhhhhhhh-------------------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhh--hcc
Confidence            65544443                               234899999999999999999999999999998888  489


Q ss_pred             CCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccc
Q psy3345         726 LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE  766 (787)
Q Consensus       726 ~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~  766 (787)
                      .++|.|+|.|.+..+|.++..... ...+.-+.+.|....|
T Consensus       775 kpkg~a~v~y~~ea~~s~~~~s~d-~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  775 KPKGKARVDYNTEADASRKVASVD-VAGKRENNGEVQVSNP  814 (881)
T ss_pred             ccccceeccCCCcchhhhhcccch-hhhhhhcCccccccCC
Confidence            999999999999999999999886 5666677777777554

>smart00360 RRM RNA recognition motif

Probab=99.13  E-value=2.6e-10  Score=91.48  Aligned_cols=70  Identities=44%  Similarity=0.652  Sum_probs=66.2

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       341 V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      |+|||..+++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|..|++.+++..+.|+.|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            5799999999999999999999999999988777899999999999999999999999999999999887

>KOG0113|consensus

Probab=99.12  E-value=2e-10  Score=111.46  Aligned_cols=78  Identities=23%  Similarity=0.393  Sum_probs=73.8

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      --+||.-     |+|.++|..|+..|+.||.|..|+|+.++ +|+++|||||.|+.+-|-..|.+..+|..|+|+.|-|.
T Consensus       102 ~TLFv~R-----LnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen  102 KTLFVAR-----LNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             ceeeeee-----ccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            3478888     99999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +-..
T Consensus       177 vERg  180 (335)
T KOG0113|consen  177 VERG  180 (335)
T ss_pred             eccc
Confidence            8765

>KOG0111|consensus

Probab=99.11  E-value=4.9e-11  Score=110.09  Aligned_cols=83  Identities=28%  Similarity=0.540  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ...++|||++|..++|+.-|...|-+||.|.+|.++.|-.+++++|||||+|...++|..|+..||+..+.||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy3345         414 KPK  416 (787)
Q Consensus       414 ~~~  416 (787)
                      .|.
T Consensus        88 kP~   90 (298)
T KOG0111|consen   88 KPE   90 (298)
T ss_pred             CCc
Confidence            875

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.10  E-value=5.2e-10  Score=90.60  Aligned_cols=74  Identities=34%  Similarity=0.642  Sum_probs=67.7

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      +|+|.|||..+++++|+++|+.||.|..+.+..+.  .+.++|+|||.|.+.++|..|+..++ +..+.|++|.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~--~~~~~~~~~v~f~s~~~a~~a~~~~~-~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK--DTKSKGFAFVEFEDEEDAEKALEALN-GKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC--CCCcceEEEEEECCHHHHHHHHHHhC-CCeECCeEEEEeC
Confidence            48999999999999999999999999999998874  44678999999999999999999997 6889999999875

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG4660|consensus

Probab=99.07  E-value=1.4e-09  Score=115.00  Aligned_cols=175  Identities=17%  Similarity=0.195  Sum_probs=109.2

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ....++|+|-|||..+++++|+.+|+.||+|..|+...     ...|.+||+|-+..+|++|+++|++..|.|+.|. ++
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k-~~  145 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK-RP  145 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc-CC
Confidence            44577999999999999999999999999999976643     3567999999999999999999999999999988 22


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC-CCcEEEEEeC
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFL  491 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~-~~~~a~V~F~  491 (787)
                      ...........+  ..-+........+.+...-....++.- |++.....-+...++-+|.+.. ...+ -...-+++|.
T Consensus       146 ~~~~~~~~~~~~--~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~  221 (549)
T KOG4660|consen  146 GGARRAMGLQSG--TSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFA  221 (549)
T ss_pred             Ccccccchhccc--chhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-ccccchhhhhhhhhc
Confidence            111100000000  000000000000111111112222222 7777777666677777887765 3322 2235677887


Q ss_pred             CHHHHHHHHHHhcCCeeCCeeEEEEEe
Q psy3345         492 QKNQAKAAFNSLAYTKFKEVPLYLEWA  518 (787)
Q Consensus       492 ~~~~A~~A~~~l~~~~~~g~~l~v~~~  518 (787)
                      +..++..+.... |..+.+......+.
T Consensus       222 ~~~s~a~~~~~~-G~~~s~~~~v~t~S  247 (549)
T KOG4660|consen  222 DNRSYAFSEPRG-GFLISNSSGVITFS  247 (549)
T ss_pred             cccchhhcccCC-ceecCCCCceEEec
Confidence            777775554432 55555666555554

>KOG0108|consensus

Probab=99.03  E-value=4.9e-10  Score=119.59  Aligned_cols=80  Identities=34%  Similarity=0.566  Sum_probs=77.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      +.|||+|+|+++++++|..+|+..|.|.+++++.|+.||+++||||++|.+.++|..|++.|||..+.||.|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999998754

>smart00361 RRM_1 RNA recognition motif

Probab=98.98  E-value=2.3e-09  Score=85.69  Aligned_cols=61  Identities=26%  Similarity=0.500  Sum_probs=55.4

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EecCCCC--CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         350 EDDLTKLFE----KYGPLAEVI-LPIDKET--DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       350 e~~l~~~F~----~~G~i~~v~-i~~~~~~--~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      +++|+++|+    .||.|.++. ++.++.+  +.++|||||+|.+.++|.+|++.|||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578899998    999999996 6676666  889999999999999999999999999999999876

>KOG0112|consensus

Probab=98.95  E-value=8e-10  Score=122.31  Aligned_cols=164  Identities=16%  Similarity=0.274  Sum_probs=137.7

Q ss_pred             cCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy3345         575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDE  654 (787)
Q Consensus       575 ~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g  654 (787)
                      .......+||++||+..+++.+|+..|..+|.|..|.|..-..      +...-||||.|.+...+-.|...+.+..|..
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~------~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~  440 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI------KTESAYAFVSLLNTDMTPSAKFEESGPLIGN  440 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC------CcccchhhhhhhccccCcccchhhcCCcccc
Confidence            3455678999999999999999999999999999999876432      3445699999999999999999999988876


Q ss_pred             eEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEE
Q psy3345         655 HQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE  734 (787)
Q Consensus       655 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~  734 (787)
                      -.+++.+...                ...+.+.+++++|+.-.....|...|..||.|..|.+-..       --||+|.
T Consensus       441 g~~r~glG~~----------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-------q~yayi~  497 (975)
T KOG0112|consen  441 GTHRIGLGQP----------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-------QPYAYIQ  497 (975)
T ss_pred             Cccccccccc----------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-------Ccceeee
Confidence            6666555432                2346788999999999999999999999999988766333       2499999


Q ss_pred             ecCHHHHHHHHHHhcCCeeecC--ceEEEEEccccc
Q psy3345         735 FITKNEAKRAMKALCQSTHLYG--RRLVLEWAEEAD  768 (787)
Q Consensus       735 F~~~~~A~~Al~~l~~~~~~~G--r~l~v~~A~~~~  768 (787)
                      |.++..|+.|+..|. |..|+|  ++|.|.||.+.-
T Consensus       498 yes~~~aq~a~~~~r-gap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  498 YESPPAAQAATHDMR-GAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             cccCccchhhHHHHh-cCcCCCCCcccccccccCCC
Confidence            999999999999997 799988  889999998543

>KOG4660|consensus

Probab=98.95  E-value=3.6e-09  Score=111.88  Aligned_cols=71  Identities=20%  Similarity=0.296  Sum_probs=65.2

Q ss_pred             cCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC-CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEE
Q psy3345         444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  514 (787)
Q Consensus       444 ~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~-~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~  514 (787)
                      .....+|+|-|||..++.++|..+|+.||+|..|...+ ..+.+||+|-+.-+|++|++.|+++++.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            34568899999999999999999999999999988877 457999999999999999999999999998887

>KOG4661|consensus

Probab=98.90  E-value=2e-09  Score=112.52  Aligned_cols=80  Identities=19%  Similarity=0.211  Sum_probs=74.2

Q ss_pred             EEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEcc
Q psy3345          16 SLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCS   94 (787)
Q Consensus        16 ~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~   94 (787)
                      .-+||||.+|...+-..||+.+|++||.|...+++.+- ...-|+|+||++.+.++|.+||..||.+.+.||.|.|+.++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            34788888899999999999999999999999999865 66789999999999999999999999999999999999998


Q ss_pred             C
Q psy3345          95 N   95 (787)
Q Consensus        95 ~   95 (787)
                      .
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            5

>KOG0128|consensus

Probab=98.90  E-value=2.9e-11  Score=133.09  Aligned_cols=322  Identities=18%  Similarity=0.145  Sum_probs=225.8

Q ss_pred             ccceEEEeCCCCCCCHHhHH-HhhcCCCCc--ceeec----ccceEEEeecChHhHHHHHhcCCcc-cCCeeEEEeeccc
Q psy3345         223 QYHTIVVKNLPAGVKKKDLK-AYFKPLPLA--SVRTT----FLGMAYIGFKDEKNCNKALNKNKSF-WKGKQLNIYKYSK  294 (787)
Q Consensus       223 ~~~~v~v~nLp~~~te~di~-~~F~~~g~v--~i~i~----~~g~afV~F~~~~~A~~Al~~~~~~-l~g~~i~v~~~~~  294 (787)
                      -.++..|-|-|..-....|. .|+.-++.+  .+.+.    ..+.||+.-..++++..++.....+ -..-.+.++    
T Consensus       478 md~~R~iWn~imty~~~~iag~Wle~~~lE~~~g~~~~~R~~~R~ay~~~~~~~~~~ev~~~~~r~Ere~gtl~~~----  553 (881)
T KOG0128|consen  478 MDKAREIWNFIMTYGGGSIAGKWLEAINLEREYGDGPSARKVLRKAYSQVVDPEDALEVLEFFRRFEREYGTLESF----  553 (881)
T ss_pred             hhhhhHhhhccccCCcchHHHHHHHHHhHHHHhCCchhHHHHHHHHHhcCcCchhHHHHHHHHHHHHhccccHHHH----
Confidence            34567788888888888888 777766554  23333    3368888889999888888733211 111111110    


Q ss_pred             CCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHH-HHHHHHHhcCCeeEEEEecCCC
Q psy3345         295 DNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTED-DLTKLFEKYGPLAEVILPIDKE  373 (787)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~-~l~~~F~~~G~i~~v~i~~~~~  373 (787)
                                        ........+      .............+.++-+..... ..+..|..+|.+..|.++....
T Consensus       554 ------------------~~~~~~~~p------r~~~~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~  609 (881)
T KOG0128|consen  554 ------------------DLCPEKVLP------RVYEAPLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGF  609 (881)
T ss_pred             ------------------hhhHHhhcc------hhhhhhhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccc
Confidence                              000000000      000111223456677777766665 5677899999999999875322


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEe
Q psy3345         374 TDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK  453 (787)
Q Consensus       374 ~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~  453 (787)
                      .-..-.++++.+.....+..|.. ..+..+.++...+..+.+.+......    .           .+...+...+++++
T Consensus       610 k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~~~~~~~~k----v-----------s~n~~R~~~~~fvs  673 (881)
T KOG0128|consen  610 KAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLADAEEKEENFK----V-----------SPNEIRDLIKIFVS  673 (881)
T ss_pred             cccccchhhhhhccccchhhccc-ccccccCCccccCCCCCchhhhhccC----c-----------CchHHHHHHHHHHh
Confidence            11122288999999999999985 67778888888887776552211100    0           01112345678999


Q ss_pred             CCCCCCCHHHHHHhhccCCCeeEEEec--C----CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccc
Q psy3345         454 NLPYRTLPTDLKALFEPFGDLGRVLVP--P----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAK  527 (787)
Q Consensus       454 nlp~~~t~~~l~~~F~~~G~v~~v~i~--~----~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~  527 (787)
                      ||+..+.+.+|...|..+|.+..+.+.  .    -+|.|||.|..+++|.+|+....++.++                  
T Consensus       674 nl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g------------------  735 (881)
T KOG0128|consen  674 NLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG------------------  735 (881)
T ss_pred             hcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh------------------
Confidence            999999999999999999988765554  1    3478999999999999998855443332                  


Q ss_pred             cccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCe
Q psy3345         528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI  607 (787)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v  607 (787)
                                                                          ...++|.|.|+..|.++++.+++.+|.+
T Consensus       736 ----------------------------------------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~  763 (881)
T KOG0128|consen  736 ----------------------------------------------------KISVAISGPPFQGTKEELKSLASKTGNV  763 (881)
T ss_pred             ----------------------------------------------------hhhhheeCCCCCCchHHHHhhccccCCc
Confidence                                                                2468999999999999999999999999


Q ss_pred             EEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCc
Q psy3345         608 ASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR  664 (787)
Q Consensus       608 ~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~  664 (787)
                      .+.+++...+      |.++|.++|.|.+..+|.++...+....+.-..+.|..+.+
T Consensus       764 ~~~~~vt~r~------gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  764 TSLRLVTVRA------GKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             cccchhhhhc------cccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            9999888776      78999999999999999999998888888888888877654

>KOG0129|consensus

Probab=98.86  E-value=2.2e-08  Score=105.09  Aligned_cols=163  Identities=18%  Similarity=0.253  Sum_probs=119.8

Q ss_pred             cCCCccceEEEeCCCCCCCHHhHHHhhcCCCCcceeec----------ccc---eEEEeecChHhHHHHHhcCCcccCCe
Q psy3345         219 VHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTT----------FLG---MAYIGFKDEKNCNKALNKNKSFWKGK  285 (787)
Q Consensus       219 ~~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~----------~~g---~afV~F~~~~~A~~Al~~~~~~l~g~  285 (787)
                      ...+-++-|+|++||++++|+.|...|..||.+.|...          ++|   |+|+-|.++...+..+.---..-.+-
T Consensus       254 ~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~  333 (520)
T KOG0129|consen  254 RSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNY  333 (520)
T ss_pred             CccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccce
Confidence            34566788999999999999999999999998765544          566   99999999999988776111111223


Q ss_pred             eEEEeecccCCccccCCCcCCCCchhhhhhhhccccc--ccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHH-hcCC
Q psy3345         286 QLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKS--QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFE-KYGP  362 (787)
Q Consensus       286 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~  362 (787)
                      ++.|.  .+....              ......+|.-  ..-..+....+.+.++|||++||..++-++|..+|. -||.
T Consensus       334 yf~vs--s~~~k~--------------k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGg  397 (520)
T KOG0129|consen  334 YFKVS--SPTIKD--------------KEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGG  397 (520)
T ss_pred             EEEEe--cCcccc--------------cceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCc
Confidence            33331  000000              0022224421  111122344567789999999999999999999999 7999


Q ss_pred             eeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHH
Q psy3345         363 LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH  397 (787)
Q Consensus       363 i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~  397 (787)
                      |..+-|-.|++-+.++|-|-|+|.+.....+||++
T Consensus       398 V~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  398 VLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             eEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            99999999977899999999999999999999974

>KOG0415|consensus

Probab=98.84  E-value=4.6e-09  Score=104.05  Aligned_cols=84  Identities=23%  Similarity=0.388  Sum_probs=79.5

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      .++...|||..|.+-+|.++|.-+|+.||+|.+|.|+++..||.+..||||+|.+.+++.+|.-.|++..|..+.|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy3345         413 GKPK  416 (787)
Q Consensus       413 ~~~~  416 (787)
                      +..-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            7653

>KOG4210|consensus

Probab=98.84  E-value=2.4e-09  Score=109.38  Aligned_cols=180  Identities=25%  Similarity=0.309  Sum_probs=144.7

Q ss_pred             CCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEE
Q psy3345         578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI  657 (787)
Q Consensus       578 ~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l  657 (787)
                      ...+++|++++...+.+.+...++..+|....+......+     ...++|++.+.|...+.+..|+.......+.+..+
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~-----~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~  160 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLED-----SLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKG  160 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhcc-----ccccccceeeccccHHHHHHHHHhhhccccccccc
Confidence            3468999999999999998999999999887777766444     46799999999999999999999554467788877


Q ss_pred             EEEecCccccchhhhhhhccccccCCCCCEEE-EecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEec
Q psy3345         658 ELKRSNRNLESEATTVKRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI  736 (787)
Q Consensus       658 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~  736 (787)
                      ...+.......    ...........+..+++ |.||++.+++++|+..|..+|.|..++++.+. .+|.++|||+|+|.
T Consensus       161 ~~dl~~~~~~~----~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~-~s~~~kg~a~~~~~  235 (285)
T KOG4210|consen  161 EKDLNTRRGLR----PKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDE-ESGDSKGFAYVDFS  235 (285)
T ss_pred             cCccccccccc----ccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCC-Cccchhhhhhhhhh
Confidence            77666543321    11111112223344455 99999999999999999999999999999986 89999999999999


Q ss_pred             CHHHHHHHHHHhcCCeeecCceEEEEEcccccc
Q psy3345         737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       737 ~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~  769 (787)
                      ....+..|+.. . ...+.|+.+++.+..+...
T Consensus       236 ~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  236 AGNSKKLALND-Q-TRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             hchhHHHHhhc-c-cCcccCcccccccCCCCcc
Confidence            99999999987 5 5899999999999987643

>KOG0415|consensus

Probab=98.84  E-value=4.5e-09  Score=104.10  Aligned_cols=82  Identities=20%  Similarity=0.301  Sum_probs=78.6

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +.|.+.++|+.     |-+-+|.+||.-+||.||.|..|.+++++ +|-+-.||||.|.+.+++++|.=+|++..|+.|+
T Consensus       236 ~PPeNVLFVCK-----LNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrR  310 (479)
T KOG0415|consen  236 KPPENVLFVCK-----LNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRR  310 (479)
T ss_pred             CCCcceEEEEe-----cCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccce
Confidence            45889999999     99999999999999999999999999988 8999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |+|.++..
T Consensus       311 IHVDFSQS  318 (479)
T KOG0415|consen  311 IHVDFSQS  318 (479)
T ss_pred             EEeehhhh
Confidence            99999875

>KOG0129|consensus

Probab=98.79  E-value=1.7e-07  Score=98.64  Aligned_cols=165  Identities=21%  Similarity=0.310  Sum_probs=121.8

Q ss_pred             CCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCccc---EEEEEeCCHHHHHHHHHHhCCCcc
Q psy3345         576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMG---YGFVQFYTRESLNQALKVLQNSSL  652 (787)
Q Consensus       576 ~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G---~afV~F~~~e~A~~A~~~lng~~l  652 (787)
                      ...-.+.|||++||.+++++.|...|..||.+. +.-+....  ..+...++|   |.|+.|.+......-+.++   ..
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~--~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC---~~  328 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKAN--SRGRAPPKGSYGYVFLVFEDERSVQSLLSAC---SE  328 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceE-eecCCCcc--ccccCCCCCcccEEEEEecchHHHHHHHHHH---hh
Confidence            345568999999999999999999999999753 22221111  112223445   9999999999888777754   33


Q ss_pred             CCeEEEEEecCccccchhh---------hhhhccccccCCCCCEEEEecCCccCcHHHHHHHHH-hcCCeeEEEeccccC
Q psy3345         653 DEHQIELKRSNRNLESEAT---------TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFK-AFGELKFVRLPKKMV  722 (787)
Q Consensus       653 ~g~~l~v~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~-~~G~I~~v~i~~~~~  722 (787)
                      +...+.++.+.+.......         ...-.....+-.+.++|||++||--+|.++|-.+|+ -||.|..+.|-.|+ 
T Consensus       329 ~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~-  407 (520)
T KOG0129|consen  329 GEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDP-  407 (520)
T ss_pred             cccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCc-
Confidence            5556666555544332110         011111334556889999999999999999999998 79999999998885 


Q ss_pred             CCCCCceEEEEEecCHHHHHHHHHH
Q psy3345         723 GSGLHRGFGFVEFITKNEAKRAMKA  747 (787)
Q Consensus       723 ~~g~~~g~afV~F~~~~~A~~Al~~  747 (787)
                      +-+.++|-|.|.|.+-++-.+||.+
T Consensus       408 k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  408 KLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccCCCCCcceeeecccHHHHHHHhh
Confidence            6788999999999999999999986

>KOG4208|consensus

Probab=98.77  E-value=3.6e-08  Score=91.40  Aligned_cols=87  Identities=24%  Similarity=0.387  Sum_probs=77.7

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhc-CCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAF-GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~-G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ......++|..+|..+-+.+|..+|.+| |.|..+++-++. .+|.++|||||+|.+++.|.-|-..|| ++.|+|+.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnk-rTGNSKgYAFVEFEs~eVA~IaAETMN-NYLl~e~lL~  123 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNK-RTGNSKGYAFVEFESEEVAKIAAETMN-NYLLMEHLLE  123 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeeccc-ccCCcCceEEEEeccHHHHHHHHHHhh-hhhhhhheee
Confidence            3456779999999999999999999988 778888887776 799999999999999999999999998 5999999999


Q ss_pred             EEEccccccH
Q psy3345         761 LEWAEEADNV  770 (787)
Q Consensus       761 v~~A~~~~~~  770 (787)
                      +.+-.|+..+
T Consensus       124 c~vmppe~~v  133 (214)
T KOG4208|consen  124 CHVMPPEQKV  133 (214)
T ss_pred             eEEeCchhhh
Confidence            9999888433

>KOG0153|consensus

Probab=98.76  E-value=2.2e-08  Score=99.65  Aligned_cols=78  Identities=19%  Similarity=0.461  Sum_probs=71.3

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      +..-++|||++|-..+++.||++.|-+||+|.++++...       +++|||+|.|.++|+.|...+-+...+.|.+|.|
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-------cccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            445689999999999999999999999999999999776       5799999999999999999865578999999999


Q ss_pred             EEccc
Q psy3345         762 EWAEE  766 (787)
Q Consensus       762 ~~A~~  766 (787)
                      .|+.+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99998

>KOG4208|consensus

Probab=98.73  E-value=3.2e-08  Score=91.79  Aligned_cols=82  Identities=22%  Similarity=0.402  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhc-CCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKY-GPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~-G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      .....++|..+|..+.+.+|..+|.+| |.+..+++-+++.||.++|||||+|.+.+.|.-|-+.||+..|.|+.|.+..
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            345579999999999999999999998 7888888889999999999999999999999999999999999999998877


Q ss_pred             CCC
Q psy3345         413 GKP  415 (787)
Q Consensus       413 ~~~  415 (787)
                      -.+
T Consensus       127 mpp  129 (214)
T KOG4208|consen  127 MPP  129 (214)
T ss_pred             eCc
Confidence            554

>KOG0226|consensus

Probab=98.66  E-value=2.6e-08  Score=94.86  Aligned_cols=169  Identities=15%  Similarity=0.224  Sum_probs=129.9

Q ss_pred             CeEEecCCCCCCCHHH-H--HHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEE
Q psy3345         581 TTLYIKNLNFNSTEDS-I--RRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI  657 (787)
Q Consensus       581 ~~l~V~NLp~~~t~~~-L--~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l  657 (787)
                      ...++.|+-..+..+- |  -..|+.|..+....++++..      +.-.+++|+.|.....-.++-..-+++.++-..+
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p------~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~V  170 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP------QPIRPEAFESFKASDALLKAETEKEKKKIGKPPV  170 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC------CccCcccccCcchhhhhhhhccccccccccCcce
Confidence            3455566555555444 2  56677777666666666543      4567899999999988888888778888877775


Q ss_pred             EEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecC
Q psy3345         658 ELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT  737 (787)
Q Consensus       658 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~  737 (787)
                      ++.-...-..        ...........+||-+.|-.+++++-|-..|.+|-.-...++.++. .+|+++|||||.|.+
T Consensus       171 R~a~gtswed--------Psl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdk-RTgKSkgygfVSf~~  241 (290)
T KOG0226|consen  171 RLAAGTSWED--------PSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDK-RTGKSKGYGFVSFRD  241 (290)
T ss_pred             eeccccccCC--------cccccCccccceeecccccccccHHHHHHHHHhccchhhccccccc-cccccccceeeeecC
Confidence            5543322111        1123445677899999999999999999999999888888888886 799999999999999


Q ss_pred             HHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         738 KNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       738 ~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      +.++.+||..|| |..++.|.|.+.-..
T Consensus       242 pad~~rAmrem~-gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  242 PADYVRAMREMN-GKYVGSRPIKLRKSE  268 (290)
T ss_pred             HHHHHHHHHhhc-ccccccchhHhhhhh
Confidence            999999999997 799999999986554

>KOG0533|consensus

Probab=98.65  E-value=7.1e-08  Score=94.64  Aligned_cols=79  Identities=23%  Similarity=0.391  Sum_probs=75.0

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      +.+|.|.|     ||+.++++||+++|..||.+..|-|-+++.|++.|.|=|.|...+||.+|++.||+..++|+.+.+.
T Consensus        83 ~~~v~v~N-----L~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   83 STKVNVSN-----LPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cceeeeec-----CCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            36688888     9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      ....
T Consensus       158 ~i~~  161 (243)
T KOG0533|consen  158 IISS  161 (243)
T ss_pred             EecC
Confidence            8775

>KOG0132|consensus

Probab=98.64  E-value=5.9e-08  Score=106.02  Aligned_cols=78  Identities=22%  Similarity=0.526  Sum_probs=72.2

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      .+++|||++|+..+++.||..+|+.||.|.+|.+...       ||+|||++...++|.+|+++|+ ...+.++.|++.|
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-------R~cAfI~M~~RqdA~kalqkl~-n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-------RGCAFIKMVRRQDAEKALQKLS-NVKVADKTIKIAW  491 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-------CceeEEEEeehhHHHHHHHHHh-cccccceeeEEee
Confidence            6899999999999999999999999999999988665       7999999999999999999998 5999999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      |....-
T Consensus       492 a~g~G~  497 (894)
T KOG0132|consen  492 AVGKGP  497 (894)
T ss_pred             eccCCc
Confidence            985443

>KOG0112|consensus

Probab=98.50  E-value=9.6e-08  Score=106.25  Aligned_cols=162  Identities=17%  Similarity=0.225  Sum_probs=138.5

Q ss_pred             ccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEe
Q psy3345         332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLI  411 (787)
Q Consensus       332 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~  411 (787)
                      +...+++||++||+..+++.+|+..|..+|.+.+|.|-+-+ -+...-||||.|.+...+-.|...+.+..|....+.+.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            34467899999999999999999999999999999885542 34555699999999999999998888887776666665


Q ss_pred             eCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeC
Q psy3345         412 PGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFL  491 (787)
Q Consensus       412 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~  491 (787)
                      +..+                           .....+.+++.+|+.......|...|..||.|..|.+.....+|+|.|.
T Consensus       447 lG~~---------------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~ye  499 (975)
T KOG0112|consen  447 LGQP---------------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYE  499 (975)
T ss_pred             cccc---------------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecc
Confidence            5432                           2334688999999999999999999999999999999998899999999


Q ss_pred             CHHHHHHHHHHhcCCeeCC--eeEEEEEecCc
Q psy3345         492 QKNQAKAAFNSLAYTKFKE--VPLYLEWAPEG  521 (787)
Q Consensus       492 ~~~~A~~A~~~l~~~~~~g--~~l~v~~~~~~  521 (787)
                      +...|+.|+..+.|..|+|  +.+.|.++...
T Consensus       500 s~~~aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  500 SPPAAQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             cCccchhhHHHHhcCcCCCCCcccccccccCC
Confidence            9999999999999999985  67888887543

>KOG0132|consensus

Probab=98.50  E-value=3e-07  Score=100.66  Aligned_cols=87  Identities=30%  Similarity=0.368  Sum_probs=77.1

Q ss_pred             CCCCcccceEEE--ecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           6 SGPVVPRNHISL--LDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         6 ~~~~~~~~~~~~--~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      +.|.++...|.|  +-|||-+||.+++|.||+.+|..||+|..|.++-.     ||+|||++..-.||.+|+.+|++..+
T Consensus       408 glP~I~pd~isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv  482 (894)
T KOG0132|consen  408 GLPTIPPDHISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKV  482 (894)
T ss_pred             cCCCCCCcceeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccc
Confidence            456665555444  56888889999999999999999999999988876     89999999999999999999999999


Q ss_pred             CCceEEEEEccCCC
Q psy3345          84 FSSRIKVEKCSNLG   97 (787)
Q Consensus        84 ~~~~i~v~~~~~~~   97 (787)
                      .++.|.|.||..+|
T Consensus       483 ~~k~Iki~Wa~g~G  496 (894)
T KOG0132|consen  483 ADKTIKIAWAVGKG  496 (894)
T ss_pred             cceeeEEeeeccCC
Confidence            99999999998754

>KOG4454|consensus

Probab=98.49  E-value=4e-08  Score=91.31  Aligned_cols=137  Identities=22%  Similarity=0.350  Sum_probs=116.1

Q ss_pred             CCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Q psy3345         580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIEL  659 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v  659 (787)
                      .++|||.|+...++++-|.++|-+.|+|..|.|+...+      +..+ ||||.|.+.-...-|+..+||..+.+..+.+
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d------~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~   81 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD------QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQR   81 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc------CCCc-eeeeecccccchhhhhhhcccchhccchhhc
Confidence            47999999999999999999999999999999998877      3444 9999999999999999999999999999988


Q ss_pred             EecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHH
Q psy3345         660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN  739 (787)
Q Consensus       660 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~  739 (787)
                      ++-.-...                       --|...++.+.+.+.|+.-|.+..++++++  .+|+++.++||.+-...
T Consensus        82 ~~r~G~sh-----------------------apld~r~~~ei~~~v~s~a~p~~~~R~~~~--~d~rnrn~~~~~~qr~~  136 (267)
T KOG4454|consen   82 TLRCGNSH-----------------------APLDERVTEEILYEVFSQAGPIEGVRIPTD--NDGRNRNFGFVTYQRLC  136 (267)
T ss_pred             ccccCCCc-----------------------chhhhhcchhhheeeecccCCCCCcccccc--ccCCccCccchhhhhhh
Confidence            77432211                       014456788888999999999999999998  46999999999998877


Q ss_pred             HHHHHHHHh
Q psy3345         740 EAKRAMKAL  748 (787)
Q Consensus       740 ~A~~Al~~l  748 (787)
                      +.-.|+...
T Consensus       137 ~~P~~~~~y  145 (267)
T KOG4454|consen  137 AVPFALDLY  145 (267)
T ss_pred             cCcHHhhhh
Confidence            777777654

>KOG4661|consensus

Probab=98.48  E-value=2.9e-07  Score=96.67  Aligned_cols=81  Identities=25%  Similarity=0.464  Sum_probs=73.7

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ..+++|+|.+|...+...||+.+|++||.|+-.+|+.+....| .++||||++.+..+|.++|..|+ .+.|+||-|.|+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPG-aRCYGfVTMSts~eAtkCI~hLH-rTELHGrmISVE  480 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPG-ARCYGFVTMSTSAEATKCIEHLH-RTELHGRMISVE  480 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCC-cceeEEEEecchHHHHHHHHHhh-hhhhcceeeeee
Confidence            4678999999999999999999999999999999988853333 58999999999999999999995 799999999999


Q ss_pred             Ecc
Q psy3345         763 WAE  765 (787)
Q Consensus       763 ~A~  765 (787)
                      -|+
T Consensus       481 kaK  483 (940)
T KOG4661|consen  481 KAK  483 (940)
T ss_pred             ecc
Confidence            987

>KOG4210|consensus

Probab=98.41  E-value=3.4e-07  Score=93.77  Aligned_cols=169  Identities=23%  Similarity=0.303  Sum_probs=127.9

Q ss_pred             CccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-------ccceEEEeecChHhHHHHHhcCCc-ccCCeeEEEeec
Q psy3345         222 RQYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-------FLGMAYIGFKDEKNCNKALNKNKS-FWKGKQLNIYKY  292 (787)
Q Consensus       222 ~~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-------~~g~afV~F~~~~~A~~Al~~~~~-~l~g~~i~v~~~  292 (787)
                      +...+.+++++...+.+.++..++...|.. ...+.       .+|++++.|...+.+..||...+. .+.++.+..-  
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~d--  163 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKD--  163 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCc--
Confidence            467889999999999999888999888754 33322       679999999999999999997664 3444443330  


Q ss_pred             ccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEE-EcCCCCCCCHHHHHHHHHhcCCeeEEEEecC
Q psy3345         293 SKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIF-VRNLSYTVTEDDLTKLFEKYGPLAEVILPID  371 (787)
Q Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~  371 (787)
                          .....                 ..  ...............++| |++|++.+++++|+.+|..+|.|..++++.+
T Consensus       164 ----l~~~~-----------------~~--~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~  220 (285)
T KOG4210|consen  164 ----LNTRR-----------------GL--RPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTD  220 (285)
T ss_pred             ----ccccc-----------------cc--cccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCC
Confidence                00000                 00  000000011223344555 9999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         372 KETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       372 ~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      ..++.++|||||.|.....+..++.. ....+.++++.+....+.
T Consensus       221 ~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  221 EESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             CCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCC
Confidence            99999999999999999999999976 788999999999887654

>KOG0226|consensus

Probab=98.41  E-value=4.2e-07  Score=86.79  Aligned_cols=129  Identities=26%  Similarity=0.383  Sum_probs=98.7

Q ss_pred             ccceEEEeecChHhHHHHHh-cCCcccCCeeEEEeecccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCC
Q psy3345         257 FLGMAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAE  335 (787)
Q Consensus       257 ~~g~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  335 (787)
                      -.+.+|+.|.....-.++-. .+++.++.++|.+-   .       +.       +-.......|.            ..
T Consensus       139 ~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a---~-------gt-------swedPsl~ew~------------~~  189 (290)
T KOG0226|consen  139 IRPEAFESFKASDALLKAETEKEKKKIGKPPVRLA---A-------GT-------SWEDPSLAEWD------------ED  189 (290)
T ss_pred             cCcccccCcchhhhhhhhccccccccccCcceeec---c-------cc-------ccCCcccccCc------------cc
Confidence            34788998888777766666 45666666665551   0       00       00011111222            23


Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      ..+||-+.|..+++++.|-..|.+|-......+++++.||+++||+||.|.+..++.+|++.|+|..++.++|.+.-+.
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            4589999999999999999999999888888999999999999999999999999999999999999999999886544

>KOG0533|consensus

Probab=98.39  E-value=1e-06  Score=86.54  Aligned_cols=83  Identities=30%  Similarity=0.477  Sum_probs=75.8

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|+|.|||..++++||+++|..||.++.+-|-.+  ..|.+.|.|=|.|...++|..|++.++ +..+.|+.|.+..
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~--~~G~s~Gta~v~~~r~~DA~~avk~~~-gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD--RAGRSLGTADVSFNRRDDAERAVKKYN-GVALDGRPMKIEI  158 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC--CCCCCCccceeeecchHhHHHHHHHhc-CcccCCceeeeEE
Confidence            4478999999999999999999999999988888887  599999999999999999999999997 5999999999998


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      ..+...
T Consensus       159 i~~~~~  164 (243)
T KOG0533|consen  159 ISSPSQ  164 (243)
T ss_pred             ecCccc
Confidence            875553

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.38  E-value=3e-06  Score=70.97  Aligned_cols=79  Identities=23%  Similarity=0.392  Sum_probs=69.3

Q ss_pred             CEEEEecCCccCcHHHHHHHHHh--cCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec----CceE
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKA--FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY----GRRL  759 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~--~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~----Gr~l  759 (787)
                      ++|.|+|||...|.++|.+++..  .|...-+.+|.|+ .++.+.|||||.|.+++.|.+-.+.++ |..+.    .+..
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf-~~~~N~GYAFVNf~~~~~~~~F~~~f~-g~~w~~~~s~Kvc   79 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDF-KNKCNLGYAFVNFTSPQAAIRFYKAFN-GKKWPNFNSKKVC   79 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeec-cCCCceEEEEEEcCCHHHHHHHHHHHc-CCccccCCCCcEE
Confidence            68999999999999999999974  3777889999997 788899999999999999999999997 56554    4788


Q ss_pred             EEEEccc
Q psy3345         760 VLEWAEE  766 (787)
Q Consensus       760 ~v~~A~~  766 (787)
                      .|.||+-
T Consensus        80 ~i~yAri   86 (97)
T PF04059_consen   80 EISYARI   86 (97)
T ss_pred             EEehhHh
Confidence            9999973

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.32  E-value=3.9e-06  Score=70.30  Aligned_cols=79  Identities=22%  Similarity=0.425  Sum_probs=68.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC----CeEEEE
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKY--GPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFL----GRMLHL  410 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~----g~~l~v  410 (787)
                      ++|.|+|+|...|.++|.+++...  |...-+.++.|..++.+.|||||.|.+++.|.+-.+.++|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            489999999999999999988653  67777899999889999999999999999999999999998774    467777


Q ss_pred             eeCCC
Q psy3345         411 IPGKP  415 (787)
Q Consensus       411 ~~~~~  415 (787)
                      .+|.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77763

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0153|consensus

Probab=98.32  E-value=1.3e-06  Score=87.42  Aligned_cols=81  Identities=17%  Similarity=0.304  Sum_probs=72.5

Q ss_pred             hhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHh-cCCeeCCeeEEEEEe
Q psy3345         440 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL-AYTKFKEVPLYLEWA  518 (787)
Q Consensus       440 ~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l-~~~~~~g~~l~v~~~  518 (787)
                      .++.....++|+|++|-..+++.+|+++|-+||+|.++.+.+..+.|||+|.+.+.|+.|..++ +...+.|..|.|.|+
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3445667899999999999999999999999999999999999999999999999999987765 556688999999999


Q ss_pred             cC
Q psy3345         519 PE  520 (787)
Q Consensus       519 ~~  520 (787)
                      ..
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            76

>KOG4454|consensus

Probab=98.21  E-value=2.6e-07  Score=86.00  Aligned_cols=141  Identities=22%  Similarity=0.299  Sum_probs=113.9

Q ss_pred             CCccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-----ccceEEEeecChHhHHHHHh-cCCcccCCeeEEEeecc
Q psy3345         221 KRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-----FLGMAYIGFKDEKNCNKALN-KNKSFWKGKQLNIYKYS  293 (787)
Q Consensus       221 ~~~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-----~~g~afV~F~~~~~A~~Al~-~~~~~l~g~~i~v~~~~  293 (787)
                      ....++|+|.|+-..++|+-|.++|-..|+| .|.|.     .-.+|||.|.++-....|++ +|+..+.++.+.+.   
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~---   82 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRT---   82 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcc---
Confidence            4467899999999999999999999999998 66666     22399999999999999999 78888888888873   


Q ss_pred             cCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcC----CCCCCCHHHHHHHHHhcCCeeEEEEe
Q psy3345         294 KDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRN----LSYTVTEDDLTKLFEKYGPLAEVILP  369 (787)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----Lp~~~te~~l~~~F~~~G~i~~v~i~  369 (787)
                                                                   ++-++    |...++++.+...|+..|++..+++.
T Consensus        83 ---------------------------------------------~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~  117 (267)
T KOG4454|consen   83 ---------------------------------------------LRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIP  117 (267)
T ss_pred             ---------------------------------------------cccCCCcchhhhhcchhhheeeecccCCCCCcccc
Confidence                                                         22233    45568889999999999999999999


Q ss_pred             cCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         370 IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       370 ~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      .+.+ |+++.++|+.+......-.++....+..+.-+++.+
T Consensus       118 ~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~~  157 (267)
T KOG4454|consen  118 TDND-GRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVTI  157 (267)
T ss_pred             cccc-CCccCccchhhhhhhcCcHHhhhhcccCcCCCCccc
Confidence            8854 889999999988888888888766665544444333

>KOG0116|consensus

Probab=98.21  E-value=2.8e-06  Score=90.60  Aligned_cols=79  Identities=16%  Similarity=0.245  Sum_probs=70.1

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ....|+|+|     ||.++|+.+|+++|..||.|+...|.... .+++.+||||.|.+.+.++.||.. +-..|+++++.
T Consensus       287 ~~~~i~V~n-----lP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~  360 (419)
T KOG0116|consen  287 DGLGIFVKN-----LPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLN  360 (419)
T ss_pred             cccceEeec-----CCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEE
Confidence            344488888     99999999999999999999998888854 566669999999999999999999 89999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |+--++
T Consensus       361 Veek~~  366 (419)
T KOG0116|consen  361 VEEKRP  366 (419)
T ss_pred             EEeccc
Confidence            987654

>KOG0151|consensus

Probab=98.21  E-value=2.1e-06  Score=93.15  Aligned_cols=85  Identities=22%  Similarity=0.366  Sum_probs=75.2

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEecccc--CCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM--VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR  758 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~--~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~  758 (787)
                      ..+..++|||.||++.++++.|...|.+||.|.+++|+...  -+..+.+.+|||.|.+..+|.+|+..|+ |..+++..
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lq-g~iv~~~e  248 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQ-GIIVMEYE  248 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhc-ceeeeeee
Confidence            35678999999999999999999999999999999997654  2234567799999999999999999997 79999999


Q ss_pred             EEEEEccc
Q psy3345         759 LVLEWAEE  766 (787)
Q Consensus       759 l~v~~A~~  766 (787)
                      |++-|+++
T Consensus       249 ~K~gWgk~  256 (877)
T KOG0151|consen  249 MKLGWGKA  256 (877)
T ss_pred             eeeccccc
Confidence            99999963

>KOG0116|consensus

Probab=98.18  E-value=2.5e-06  Score=90.87  Aligned_cols=80  Identities=34%  Similarity=0.517  Sum_probs=68.6

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ....|||+|||++++..+|+++|..||.|+..+|.... ..+...+||||+|.+..+++.|+.+-  -..++|++|.|+-
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~-~~~~~~~fgFV~f~~~~~~~~~i~As--p~~ig~~kl~Vee  363 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRS-PGGKNPCFGFVEFENAAAVQNAIEAS--PLEIGGRKLNVEE  363 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEec-cCCCcCceEEEEEeecchhhhhhhcC--ccccCCeeEEEEe
Confidence            34459999999999999999999999999999887763 23444599999999999999999984  5889999999987


Q ss_pred             ccc
Q psy3345         764 AEE  766 (787)
Q Consensus       764 A~~  766 (787)
                      -++
T Consensus       364 k~~  366 (419)
T KOG0116|consen  364 KRP  366 (419)
T ss_pred             ccc
Confidence            664

>KOG4209|consensus

Probab=98.09  E-value=4.3e-06  Score=82.70  Aligned_cols=82  Identities=29%  Similarity=0.464  Sum_probs=76.0

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ..+...+||+|+.+.+|.+++..+|+.||.|..+.|+.++.+|.++|||||+|.+.+.+..|+. |+|..+.|+.+.+.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3456689999999999999999999999999999999999888999999999999999999998 999999999999988


Q ss_pred             CCC
Q psy3345         413 GKP  415 (787)
Q Consensus       413 ~~~  415 (787)
                      ...
T Consensus       177 ~r~  179 (231)
T KOG4209|consen  177 KRT  179 (231)
T ss_pred             eee
Confidence            654

>KOG4209|consensus

Probab=98.02  E-value=7.6e-06  Score=80.96  Aligned_cols=80  Identities=15%  Similarity=0.272  Sum_probs=72.9

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      +....++|.+     +-+.+|-+++..+|+.||.|..|.|+.++ .|.++|||||.|.+.+.+..||+ ||+..|.|+.|
T Consensus        99 ~d~~sv~v~n-----vd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i  172 (231)
T KOG4209|consen   99 VDAPSVWVGN-----VDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAI  172 (231)
T ss_pred             cCCceEEEec-----cccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccc
Confidence            3445578888     99999999999999999999999999999 57899999999999999999999 79999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      +|..-+-
T Consensus       173 ~vt~~r~  179 (231)
T KOG4209|consen  173 EVTLKRT  179 (231)
T ss_pred             eeeeeee
Confidence            9998764

>KOG4676|consensus

Probab=98.02  E-value=5.2e-06  Score=84.06  Aligned_cols=176  Identities=13%  Similarity=0.114  Sum_probs=117.7

Q ss_pred             cceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec----------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEeec
Q psy3345         224 YHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT----------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKY  292 (787)
Q Consensus       224 ~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~----------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~  292 (787)
                      ..+|.|.||.+++|.+++..+|.-+|.+ .++|.          ....|||.|.+...+..|-.+....+-++.|.|.+|
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            3489999999999999999999999987 66666          346999999999999999887766667788888776


Q ss_pred             ccCCcccc-------C--C---CcCCCCchhhhhhh-hcccc-------cccchhhhhcc-cCCCCeEEEcCCCCCCCHH
Q psy3345         293 SKDNSAKY-------S--G---AADDNNNASMENIK-AKHWK-------SQEDSVQFAED-IAESGRIFVRNLSYTVTED  351 (787)
Q Consensus       293 ~~~~~~~~-------~--~---~~~~~~~~~~~~~~-~~~~~-------~~~~~~~~~~~-~~~~~~l~V~nLp~~~te~  351 (787)
                      .....+..       +  .   ..+........... ..+..       +.......... ..-.++++|.+|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            55444421       0  0   00000000000000 00000       00000000000 1113679999999999999


Q ss_pred             HHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q psy3345         352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFL  404 (787)
Q Consensus       352 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~  404 (787)
                      ++.+.|..+|.+...++.    .|-..-+|-+.|........|+. ++|..+.
T Consensus       167 e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            999999999998877763    34445578899999999999986 6777665

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.01  E-value=2.5e-05  Score=61.83  Aligned_cols=68  Identities=22%  Similarity=0.400  Sum_probs=47.6

Q ss_pred             CEEEEecCCccCcHHH----HHHHHHhcC-CeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         686 SKILVRNIPFQAKQSE----VEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~d----L~~~F~~~G-~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      +-|+|.|||...+...    |++++..+| .|.+|           +.+.|+|.|.+.+.|.+|...|+ |..++|++|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----------~~~tAilrF~~~~~A~RA~KRme-gEdVfG~kI~   70 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----------SGGTAILRFPNQEFAERAQKRME-GEDVFGNKIS   70 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------------TT-EEEEESSHHHHHHHHHHHT-T--SSSS--E
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----------eCCEEEEEeCCHHHHHHHHHhhc-ccccccceEE
Confidence            4699999999887654    777777886 45433           23679999999999999999997 7999999999


Q ss_pred             EEEcc
Q psy3345         761 LEWAE  765 (787)
Q Consensus       761 v~~A~  765 (787)
                      |+|..
T Consensus        71 v~~~~   75 (90)
T PF11608_consen   71 VSFSP   75 (90)
T ss_dssp             EESS-
T ss_pred             EEEcC
Confidence            99985

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.93  E-value=3.1e-05  Score=66.70  Aligned_cols=86  Identities=23%  Similarity=0.417  Sum_probs=53.7

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC----CeeecCceEE
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ----STHLYGRRLV  760 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~----~~~~~Gr~l~  760 (787)
                      ++.|+|.+++..++.++|++.|+.||.|..|.+.+.       -..|+|.|.+++.|+.|+..+..    +..+.|..+.
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~   73 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVT   73 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEE
Confidence            367899999999999999999999999999988654       23699999999999999998752    2356778888


Q ss_pred             EEEccccccHHHHHHHH
Q psy3345         761 LEWAEEADNVEDIRKRT  777 (787)
Q Consensus       761 v~~A~~~~~~~~~~~~~  777 (787)
                      ++.-..+++.+.+.+..
T Consensus        74 ~~vLeGeeE~~Yw~ki~   90 (105)
T PF08777_consen   74 LEVLEGEEEEEYWKKII   90 (105)
T ss_dssp             EE---HHHHHHHHHHHH
T ss_pred             EEECCCHHHHHHHHHHH
Confidence            88877777666654443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4676|consensus

Probab=97.93  E-value=1e-05  Score=81.94  Aligned_cols=193  Identities=16%  Similarity=0.117  Sum_probs=123.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCC---------cEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEE
Q psy3345         447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG---------ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  517 (787)
Q Consensus       447 ~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---------~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  517 (787)
                      ...|-|.||.+.++.++++.+|.-.|.|..+.+.++-         ..|||.|.+...+..| +.|-++.|-++.|.|-.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~va-QhLtntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVA-QHLTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHH-hhhccceeeeeeEEEEe
Confidence            3489999999999999999999999999988887632         3699999999888877 55888888899998887


Q ss_pred             ecCccccccccc------cccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCC
Q psy3345         518 APEGVFAEAKEK------SKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN  591 (787)
Q Consensus       518 ~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~  591 (787)
                      +...+....+.-      ...+...+.+..++........+....+...+   ..+...........-.++++|.+|+..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailkt---P~Lp~~~~A~kleeirRt~~v~sl~~~  162 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKT---PELPPQAAAKKLEEIRRTREVQSLISA  162 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecC---CCCChHhhhhhhHHHHhhhhhhcchhh
Confidence            766643333110      00111111111111111110111000000000   000000000111112378999999999


Q ss_pred             CCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy3345         592 STEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD  653 (787)
Q Consensus       592 ~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~  653 (787)
                      +...++.+.|..+|.|........         ...-+|.|+|........|+. ++|..+.
T Consensus       163 ~~l~e~~e~f~r~Gev~ya~~ask---------~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  163 AILPESGESFERKGEVSYAHTASK---------SRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hcchhhhhhhhhcchhhhhhhhcc---------CCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            999999999999999988776543         334578899999999999998 5676665

>KOG0151|consensus

Probab=97.90  E-value=1.8e-05  Score=86.09  Aligned_cols=86  Identities=30%  Similarity=0.425  Sum_probs=75.3

Q ss_pred             CCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCe
Q psy3345         576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH  655 (787)
Q Consensus       576 ~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~  655 (787)
                      .....++|||+||++.++++.|...|..||+|.+++|+--..  .....+.+-+|||-|-+..+|.+|++.|+|..+.+.
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRt--EeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRT--EEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccc--hhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            355678999999999999999999999999999999986432  122356677999999999999999999999999999


Q ss_pred             EEEEEecC
Q psy3345         656 QIELKRSN  663 (787)
Q Consensus       656 ~l~v~~~~  663 (787)
                      .+++.|+.
T Consensus       248 e~K~gWgk  255 (877)
T KOG0151|consen  248 EMKLGWGK  255 (877)
T ss_pred             eeeecccc
Confidence            99999984

>KOG2193|consensus

Probab=97.84  E-value=2e-06  Score=87.65  Aligned_cols=152  Identities=20%  Similarity=0.295  Sum_probs=121.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCc-eeCCeEEEEeeCCCC
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGT-VFLGRMLHLIPGKPK  416 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~-~~~g~~l~v~~~~~~  416 (787)
                      .+|++||.+.++..+|..+|.....-..-.++.      -.|||||.+.+...|.+|++.++|. .+.|..+.+..+.++
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            689999999999999999997552111111111      3469999999999999999999986 789999999876654


Q ss_pred             CCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC-CC--cEEEEEeCCH
Q psy3345         417 ENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YG--ITGLVEFLQK  493 (787)
Q Consensus       417 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~-~~--~~a~V~F~~~  493 (787)
                                                 ....+.+-++|+|.....+.|..+...||.+..|.... +.  ...-|+|.+.
T Consensus        77 ---------------------------kqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~  129 (584)
T KOG2193|consen   77 ---------------------------KQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQ  129 (584)
T ss_pred             ---------------------------HHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHH
Confidence                                       12244588999999999999999999999998766533 22  2345789999


Q ss_pred             HHHHHHHHHhcCCeeCCeeEEEEEecCcc
Q psy3345         494 NQAKAAFNSLAYTKFKEVPLYLEWAPEGV  522 (787)
Q Consensus       494 ~~A~~A~~~l~~~~~~g~~l~v~~~~~~~  522 (787)
                      +.++.|+.+|+|-.+....+.+.|.|...
T Consensus       130 ~~~~~ai~kl~g~Q~en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  130 QQHRQAIHKLNGPQLENQHLKVGYIPDEQ  158 (584)
T ss_pred             HHHHHHHHhhcchHhhhhhhhcccCchhh
Confidence            99999999999999999999999887653

>KOG2193|consensus

Probab=97.84  E-value=2.4e-06  Score=87.07  Aligned_cols=153  Identities=21%  Similarity=0.333  Sum_probs=120.4

Q ss_pred             CeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCC-ccCCeEEEE
Q psy3345         581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNS-SLDEHQIEL  659 (787)
Q Consensus       581 ~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~-~l~g~~l~v  659 (787)
                      ..+|++||.+..+.++|..+|...-      +..     ...--.-.||+||.+.+...|.+|++.++|. .+.|.++.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak------~~~-----~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~   70 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAK------IPG-----SGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEV   70 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcccc------CCC-----CcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeec
Confidence            3589999999999999999997531      110     0001123589999999999999999999995 588999998


Q ss_pred             EecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEe-ccccCCCCCCceEEEEEecCH
Q psy3345         660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRL-PKKMVGSGLHRGFGFVEFITK  738 (787)
Q Consensus       660 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i-~~~~~~~g~~~g~afV~F~~~  738 (787)
                      ..+-.+..                ..+.+-|+|+|+..-++-|-.+...||.+..|.. ..+     .-.-..-|.|.+.
T Consensus        71 ~~sv~kkq----------------rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~-----~etavvnvty~~~  129 (584)
T KOG2193|consen   71 EHSVPKKQ----------------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTD-----SETAVVNVTYSAQ  129 (584)
T ss_pred             cchhhHHH----------------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccc-----hHHHHHHHHHHHH
Confidence            77654333                3445889999999999999999999999998865 222     1223345899999


Q ss_pred             HHHHHHHHHhcCCeeecCceEEEEEccc
Q psy3345         739 NEAKRAMKALCQSTHLYGRRLVLEWAEE  766 (787)
Q Consensus       739 ~~A~~Al~~l~~~~~~~Gr~l~v~~A~~  766 (787)
                      +.++.||..|+ +..+....+.|.|--.
T Consensus       130 ~~~~~ai~kl~-g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen  130 QQHRQAIHKLN-GPQLENQHLKVGYIPD  156 (584)
T ss_pred             HHHHHHHHhhc-chHhhhhhhhcccCch
Confidence            99999999997 6999999999999753

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.80  E-value=0.0001  Score=58.44  Aligned_cols=68  Identities=21%  Similarity=0.351  Sum_probs=46.6

Q ss_pred             eEEEcCCCCCCCHHHHHH----HHHhcC-CeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         338 RIFVRNLSYTVTEDDLTK----LFEKYG-PLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~----~F~~~G-~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      .|+|.|||.+.+...|+.    ++..+| .|..|          +.+.|+|.|.+.+.|.+|.+.|+|..+.|+.|.|.+
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            699999999999887654    555665 56554          125799999999999999999999999999999998


Q ss_pred             CCC
Q psy3345         413 GKP  415 (787)
Q Consensus       413 ~~~  415 (787)
                      ...
T Consensus        74 ~~~   76 (90)
T PF11608_consen   74 SPK   76 (90)
T ss_dssp             S--
T ss_pred             cCC
Confidence            753

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.58  E-value=0.00021  Score=61.52  Aligned_cols=69  Identities=28%  Similarity=0.324  Sum_probs=46.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCC-----eeCCeeEEEE
Q psy3345         448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT-----KFKEVPLYLE  516 (787)
Q Consensus       448 ~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~-----~~~g~~l~v~  516 (787)
                      ..|.+.+++..++.++|++.|+.||.|..|.+.+....|+|.|.+++.|+.|+..+.-.     .+.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            46889999999999999999999999999999998899999999999999999987544     4445555444

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0115|consensus

Probab=97.48  E-value=0.00025  Score=68.51  Aligned_cols=103  Identities=19%  Similarity=0.221  Sum_probs=85.1

Q ss_pred             HHHHHHHHhCCCccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEec
Q psy3345         639 SLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP  718 (787)
Q Consensus       639 ~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~  718 (787)
                      -|..|-..|.+....|+.|+|.|+..                     ..|+|.||+.-+..+.|.+.|+.||.|....+.
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~---------------------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~   64 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH---------------------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAK   64 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc---------------------ceEEEEecchhhhhHHHHHhhhhcCccchheee
Confidence            35667777899999999999999754                     349999999999999999999999999988777


Q ss_pred             cccCCCCCCceEEEEEecCHHHHHHHHHHhcCCee---ecCceEEEEEc
Q psy3345         719 KKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH---LYGRRLVLEWA  764 (787)
Q Consensus       719 ~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~---~~Gr~l~v~~A  764 (787)
                      .|  ..+++.+-++|.|...-.|.+|+...+++-.   ..|++.-|.-+
T Consensus        65 vD--~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   65 VD--DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ec--ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            77  5899999999999999999999999865332   22455555443

>KOG1995|consensus

Probab=97.39  E-value=0.00012  Score=74.45  Aligned_cols=90  Identities=20%  Similarity=0.330  Sum_probs=78.9

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeE--------EEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL  754 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~--------v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~  754 (787)
                      ....+|||-+||..+++++|.++|.++|.|..        +.|.++. +++..+|-|.|.|.++..|+.|+.-++ +..+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dk-eT~~~KGeatvS~~D~~~akaai~~~a-gkdf  141 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDK-ETGAPKGEATVSYEDPPAAKAAIEWFA-GKDF  141 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccc-cccCcCCceeeeecChhhhhhhhhhhc-cccc
Confidence            34567999999999999999999999998754        5667776 799999999999999999999999997 7999


Q ss_pred             cCceEEEEEccccccHHHHH
Q psy3345         755 YGRRLVLEWAEEADNVEDIR  774 (787)
Q Consensus       755 ~Gr~l~v~~A~~~~~~~~~~  774 (787)
                      .|..|.|.+|+....++-++
T Consensus       142 ~gn~ikvs~a~~r~~ve~~r  161 (351)
T KOG1995|consen  142 CGNTIKVSLAERRTGVESVR  161 (351)
T ss_pred             cCCCchhhhhhhccCccccc
Confidence            99999999998777665554

>KOG2314|consensus

Probab=97.34  E-value=0.00015  Score=77.29  Aligned_cols=77  Identities=14%  Similarity=0.211  Sum_probs=61.2

Q ss_pred             cceEEEecCcccCCCccCCH-------HHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345          12 RNHISLLDLDEVEFIYKITQ-------EQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~-------~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      .+.|+|-|     .|. +-+       .-|..+|+++|.|.++.++.+..|+.+||.|+.|++..+|+.|++.|||..++
T Consensus        58 D~vVvv~g-----~Pv-V~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ld  131 (698)
T KOG2314|consen   58 DSVVVVDG-----APV-VGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLD  131 (698)
T ss_pred             ceEEEECC-----Ccc-cChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceec
Confidence            45567777     664 222       34568999999999999999998999999999999999999999999998776


Q ss_pred             C-ceEEEEEcc
Q psy3345          85 S-SRIKVEKCS   94 (787)
Q Consensus        85 ~-~~i~v~~~~   94 (787)
                      - .+..|..-+
T Consensus       132 knHtf~v~~f~  142 (698)
T KOG2314|consen  132 KNHTFFVRLFK  142 (698)
T ss_pred             ccceEEeehhh
Confidence            4 455554433

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.30  E-value=0.0005  Score=50.99  Aligned_cols=51  Identities=20%  Similarity=0.389  Sum_probs=41.4

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHH
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL   75 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~   75 (787)
                      -|.|.|     .|.+..+ ++..+|..||+|+++.+..     ..-.+||.|.+..+|++||
T Consensus         3 wI~V~G-----f~~~~~~-~vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    3 WISVSG-----FPPDLAE-EVLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             EEEEEe-----ECchHHH-HHHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            477777     8877664 4556899999999988872     3569999999999999996

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.24  E-value=0.00073  Score=67.36  Aligned_cols=86  Identities=15%  Similarity=0.239  Sum_probs=64.5

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHH------HHHhhccCceEEEEEEecC-CCCc-ceEE--EEEecCHHHHHHH
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQL------KAKFEEKGTVTDVQLKYTT-EGKF-RRFA--FIGYHREDQAQAA   74 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l------~~~f~~~g~i~~~~~~~~~-~g~~-~g~a--fv~f~~~~~a~~a   74 (787)
                      ++.-+|-.+-+.|-|     ||..+-.+++      .++|+.||.|..|.|-+.. .-.+ .+-+  ||+|.+.|||.+|
T Consensus       107 sniRVvQKNLvYVig-----i~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarc  181 (480)
T COG5175         107 SNIRVVQKNLVYVIG-----IPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARC  181 (480)
T ss_pred             ccceeeecceeEEec-----CCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHH
Confidence            444455556666666     9998877772      4899999998877665432 1111 2324  9999999999999


Q ss_pred             HHHhccCccCCceEEEEEccC
Q psy3345          75 LDYFNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        75 ~~~~~~~~~~~~~i~v~~~~~   95 (787)
                      |...||++++||.|...+...
T Consensus       182 Ia~vDgs~~DGr~lkatYGTT  202 (480)
T COG5175         182 IAEVDGSLLDGRVLKATYGTT  202 (480)
T ss_pred             HHHhccccccCceEeeecCch
Confidence            999999999999999887664

>KOG1995|consensus

Probab=97.23  E-value=0.00032  Score=71.32  Aligned_cols=84  Identities=26%  Similarity=0.389  Sum_probs=76.0

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLA--------EVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFL  404 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~  404 (787)
                      .....+|||-+||..+++.+|.++|.++|.|.        .|.|.+++.|+.++|-|.|.|.+...|+.|+..+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            44566899999999999999999999998775        3778888999999999999999999999999999999999


Q ss_pred             CeEEEEeeCCCC
Q psy3345         405 GRMLHLIPGKPK  416 (787)
Q Consensus       405 g~~l~v~~~~~~  416 (787)
                      |.+|.|.++...
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            999999888754

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.14  E-value=0.00098  Score=66.47  Aligned_cols=81  Identities=20%  Similarity=0.440  Sum_probs=63.4

Q ss_pred             CCeEEEcCCCCCCCHHHH------HHHHHhcCCeeEEEEecCCCCC-CcceE--EEEEEcCHHHHHHHHHHhCCceeCCe
Q psy3345         336 SGRIFVRNLSYTVTEDDL------TKLFEKYGPLAEVILPIDKETD-KTKGF--ALVTFLMPEHATQAYQHLDGTVFLGR  406 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l------~~~F~~~G~i~~v~i~~~~~~~-~~~g~--afV~F~~~~~A~~a~~~l~~~~~~g~  406 (787)
                      ..-+||-+||+.+..+++      .++|++||.|..|.|-+...+. .-.+.  .||+|.+.++|.+||.+.+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            346899999998877773      4799999999988775432111 11122  39999999999999999999999999


Q ss_pred             EEEEeeCCCC
Q psy3345         407 MLHLIPGKPK  416 (787)
Q Consensus       407 ~l~v~~~~~~  416 (787)
                      .|+..+...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999887654

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.11  E-value=0.0022  Score=54.35  Aligned_cols=79  Identities=15%  Similarity=0.171  Sum_probs=53.0

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEE-eccccC-----CCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVR-LPKKMV-----GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~-i~~~~~-----~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      ..+.|.|.+.|+. ....|.+.|++||.|.+.. +.++..     ..-......-|.|.++.+|.+||+.  ||+.+.|.
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~--NG~i~~g~   81 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK--NGTIFSGS   81 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT--TTEEETTC
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh--CCeEEcCc
Confidence            3567999999998 5556888999999997764 222100     0011245789999999999999997  58999997


Q ss_pred             eEE-EEEcc
Q psy3345         758 RLV-LEWAE  765 (787)
Q Consensus       758 ~l~-v~~A~  765 (787)
                      -|. |.|++
T Consensus        82 ~mvGV~~~~   90 (100)
T PF05172_consen   82 LMVGVKPCD   90 (100)
T ss_dssp             EEEEEEE-H
T ss_pred             EEEEEEEcH
Confidence            555 88875

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.08  E-value=0.0019  Score=54.70  Aligned_cols=77  Identities=21%  Similarity=0.250  Sum_probs=53.3

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEE-EEec-------CCCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQ-LKYT-------TEGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~-~~~~-------~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      +.-|.|-|     .|.. ....|-++|+.||.|.+.. +..+       +......+-.|+|.++.+|.+||.+ ||..|
T Consensus         6 ~~wVtVFG-----fp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~   78 (100)
T PF05172_consen    6 ETWVTVFG-----FPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIF   78 (100)
T ss_dssp             CCEEEEE--------GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEE
T ss_pred             CeEEEEEc-----cCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEE
Confidence            44577777     9987 5678889999999987764 1110       1112357999999999999999999 99999


Q ss_pred             CCc-eEEEEEccC
Q psy3345          84 FSS-RIKVEKCSN   95 (787)
Q Consensus        84 ~~~-~i~v~~~~~   95 (787)
                      .|. .|-|.++++
T Consensus        79 ~g~~mvGV~~~~~   91 (100)
T PF05172_consen   79 SGSLMVGVKPCDP   91 (100)
T ss_dssp             TTCEEEEEEE-HH
T ss_pred             cCcEEEEEEEcHH
Confidence            986 556777754

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.06  E-value=0.0013  Score=48.79  Aligned_cols=52  Identities=19%  Similarity=0.321  Sum_probs=44.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHH
Q psy3345         448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAF  500 (787)
Q Consensus       448 ~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~  500 (787)
                      +.|.|.+.|.+.. +.+...|..||+|..+.++......+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            4688888886655 456669999999999999988899999999999999985

>KOG0115|consensus

Probab=97.04  E-value=0.0016  Score=63.08  Aligned_cols=89  Identities=21%  Similarity=0.264  Sum_probs=78.5

Q ss_pred             HHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCccccccccccc
Q psy3345         494 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE  573 (787)
Q Consensus       494 ~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  573 (787)
                      .-|..|-..|.++...|+.+.|.|+..                                                     
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~-----------------------------------------------------   31 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH-----------------------------------------------------   31 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc-----------------------------------------------------
Confidence            346677778999999999999999943                                                     


Q ss_pred             ccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy3345         574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQ  648 (787)
Q Consensus       574 ~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~ln  648 (787)
                             ..|+|.||+..++.+.|..-|+.||+|....+..|..      +.+.|-++|.|...-.|..|...++
T Consensus        32 -------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r------~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 -------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR------GKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             -------ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc------ccccccchhhhhcchhHHHHHHHhc
Confidence                   3699999999999999999999999999988888765      6788999999999999999999874

>KOG2202|consensus

Probab=96.90  E-value=0.00043  Score=67.13  Aligned_cols=64  Identities=19%  Similarity=0.320  Sum_probs=56.5

Q ss_pred             HHHHHHhh-ccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEccC
Q psy3345          32 EQLKAKFE-EKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        32 ~~l~~~f~-~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~~   95 (787)
                      +||-..|+ +||+|+.+.|..+..-..+|-+||.|...|+|++|+..||+.++.|+.|..+++..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            45555555 88999999998877667899999999999999999999999999999999999865

>KOG3152|consensus

Probab=96.67  E-value=0.0013  Score=63.73  Aligned_cols=73  Identities=18%  Similarity=0.331  Sum_probs=62.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCC--------CCcc----eEEEEEEcCHHHHHHHHHHhCCce
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET--------DKTK----GFALVTFLMPEHATQAYQHLDGTV  402 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~--------~~~~----g~afV~F~~~~~A~~a~~~l~~~~  402 (787)
                      ....||+++||+.+...-|+++|+.||.|-.|.+-....+        |.+.    ..|+|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3558999999999999999999999999999998775544        2222    348999999999999999999999


Q ss_pred             eCCeE
Q psy3345         403 FLGRM  407 (787)
Q Consensus       403 ~~g~~  407 (787)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>KOG2314|consensus

Probab=96.61  E-value=0.0085  Score=64.33  Aligned_cols=79  Identities=20%  Similarity=0.332  Sum_probs=63.1

Q ss_pred             CCCCEEEEecCCccCc------HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC
Q psy3345         683 QTGSKILVRNIPFQAK------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG  756 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t------~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G  756 (787)
                      .-..+|+|-|+|---.      ..-|..+|+++|.|....+|.+  +.|..+||.|++|.+..+|+.|++.||+.+....
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~--e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPID--EEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccC--ccCCeeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            5578899999986432      2337889999999999999988  4677999999999999999999999985344445


Q ss_pred             ceEEEEE
Q psy3345         757 RRLVLEW  763 (787)
Q Consensus       757 r~l~v~~  763 (787)
                      +++.|..
T Consensus       134 Htf~v~~  140 (698)
T KOG2314|consen  134 HTFFVRL  140 (698)
T ss_pred             ceEEeeh
Confidence            6777654

>KOG1855|consensus

Probab=96.59  E-value=0.0057  Score=63.57  Aligned_cols=68  Identities=21%  Similarity=0.375  Sum_probs=58.0

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccc---c-CCCCCC--------ceEEEEEecCHHHHHHHHHHhc
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK---M-VGSGLH--------RGFGFVEFITKNEAKRAMKALC  749 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~---~-~~~g~~--------~g~afV~F~~~~~A~~Al~~l~  749 (787)
                      ..++++|.+.|||.+-.-+.|.++|+.+|.|.+|+|++.   + +..|.+        +-+|+|+|...+.|.+|.+.||
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            357899999999999999999999999999999999876   2 222322        4579999999999999999985

>KOG2202|consensus

Probab=96.46  E-value=0.0015  Score=63.42  Aligned_cols=62  Identities=23%  Similarity=0.291  Sum_probs=53.5

Q ss_pred             HHHHHhhc-cCCCeeEEEecCCC-----cEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccc
Q psy3345         462 TDLKALFE-PFGDLGRVLVPPYG-----ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  523 (787)
Q Consensus       462 ~~l~~~F~-~~G~v~~v~i~~~~-----~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~  523 (787)
                      +++...|+ +||+|..+.+-.+.     |.+||.|...++|++|+..||+++|.|++|..++.+..-|
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~  150 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDF  150 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCch
Confidence            56666776 89999988776644     5799999999999999999999999999999999987644

>KOG3152|consensus

Probab=96.25  E-value=0.0032  Score=61.00  Aligned_cols=78  Identities=15%  Similarity=0.276  Sum_probs=62.7

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCC---CCCCCC----cccEEEEEeCCHHHHHHHHHHhCCCc
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK---SPGQFL----SMGYGFVQFYTRESLNQALKVLQNSS  651 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~---~~~~~~----s~G~afV~F~~~e~A~~A~~~lng~~  651 (787)
                      ..-.||++|||+.+...-|+++|+.||.|-.|.+....+..   ..+.+.    ...-|.|+|.+...|.+....|||..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            34689999999999999999999999999999987765420   001122    22347899999999999999999999


Q ss_pred             cCCeE
Q psy3345         652 LDEHQ  656 (787)
Q Consensus       652 l~g~~  656 (787)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99965

>KOG1855|consensus

Probab=96.19  E-value=0.0059  Score=63.44  Aligned_cols=86  Identities=15%  Similarity=0.218  Sum_probs=65.5

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCc--------ccEEEEEeCCHHHHHHHHHHhC
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS--------MGYGFVQFYTRESLNQALKVLQ  648 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s--------~G~afV~F~~~e~A~~A~~~ln  648 (787)
                      ..+.++|.+.|||.+-.-+.|.++|+.+|.|.+|+|..-..-.....+.+        +-+|+|+|...+.|.+|...||
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            45689999999999988999999999999999999987411012223333        4569999999999999999887


Q ss_pred             CCccCCeEEEEEec
Q psy3345         649 NSSLDEHQIELKRS  662 (787)
Q Consensus       649 g~~l~g~~l~v~~~  662 (787)
                      ...-.-.-|+|.+.
T Consensus       308 ~e~~wr~glkvkLl  321 (484)
T KOG1855|consen  308 PEQNWRMGLKVKLL  321 (484)
T ss_pred             hhhhhhhcchhhhh
Confidence            65554444555443

>KOG4849|consensus

Probab=96.15  E-value=0.0052  Score=61.73  Aligned_cols=79  Identities=20%  Similarity=0.296  Sum_probs=69.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYG--PLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G--~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      .++||+||-+.+|++||.+.+...|  .+.++++..+..+|.++|||.|...+....++.++.|..+.|.|..-.|..+.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            4899999999999999999988766  56777777787889999999999999999999999999999999877777665


Q ss_pred             C
Q psy3345         415 P  415 (787)
Q Consensus       415 ~  415 (787)
                      .
T Consensus       161 K  161 (498)
T KOG4849|consen  161 K  161 (498)
T ss_pred             h
Confidence            4

>KOG1996|consensus

Probab=96.15  E-value=0.008  Score=59.16  Aligned_cols=79  Identities=20%  Similarity=0.224  Sum_probs=61.5

Q ss_pred             CCCCEEEEeCCC--CCC---CHHHHHHhhccCCCeeEEEecCCCc-------EEEEEeCCHHHHHHHHHHhcCCeeCCee
Q psy3345         445 RSKRIILVKNLP--YRT---LPTDLKALFEPFGDLGRVLVPPYGI-------TGLVEFLQKNQAKAAFNSLAYTKFKEVP  512 (787)
Q Consensus       445 ~~~~~i~v~nlp--~~~---t~~~l~~~F~~~G~v~~v~i~~~~~-------~a~V~F~~~~~A~~A~~~l~~~~~~g~~  512 (787)
                      .++.+|+++|+=  -.+   -++++...|.+||.|..|.|....+       -.||+|...++|.+|+-.|||+.|+|+.
T Consensus       279 ~ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~  358 (378)
T KOG1996|consen  279 CPTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRV  358 (378)
T ss_pred             cchHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceeccee
Confidence            345566667662  223   2467888999999999888764222       4899999999999999999999999999


Q ss_pred             EEEEEecCccc
Q psy3345         513 LYLEWAPEGVF  523 (787)
Q Consensus       513 l~v~~~~~~~~  523 (787)
                      +...|.....|
T Consensus       359 v~A~Fyn~ekf  369 (378)
T KOG1996|consen  359 VSACFYNLEKF  369 (378)
T ss_pred             eeheeccHHhh
Confidence            99988865544

>KOG1996|consensus

Probab=96.10  E-value=0.013  Score=57.69  Aligned_cols=83  Identities=19%  Similarity=0.154  Sum_probs=60.9

Q ss_pred             CCCEEEEecC--CccCc---HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce
Q psy3345         684 TGSKILVRNI--PFQAK---QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR  758 (787)
Q Consensus       684 ~~~~l~V~nL--p~~~t---~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~  758 (787)
                      +.+.|.++|+  +.+++   ++++.+.+++||.|..|-|.-.++..-.----.||+|...++|.+|+-.|| |+.|+||.
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~Vdln-GRyFGGr~  358 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLN-GRYFGGRV  358 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcC-Cceeccee
Confidence            4444666666  34444   456899999999999988765531111111136999999999999999997 89999999


Q ss_pred             EEEEEcccc
Q psy3345         759 LVLEWAEEA  767 (787)
Q Consensus       759 l~v~~A~~~  767 (787)
                      +...|...+
T Consensus       359 v~A~Fyn~e  367 (378)
T KOG1996|consen  359 VSACFYNLE  367 (378)
T ss_pred             eeheeccHH
Confidence            999998643

>KOG2416|consensus

Probab=95.96  E-value=0.0072  Score=65.27  Aligned_cols=86  Identities=15%  Similarity=0.225  Sum_probs=68.3

Q ss_pred             ccccccCCCCCEEEEecCCccCcHHHHHHHHH-hcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCee-
Q psy3345         676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFK-AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH-  753 (787)
Q Consensus       676 ~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~-~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~-  753 (787)
                      -..+.....+..|||.||=--+|..+|+.++. ..|.|...+|-+.       +..|||.|.+.++|.....+|+|-.+ 
T Consensus       435 vpSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI-------KShCyV~yss~eEA~atr~AlhnV~WP  507 (718)
T KOG2416|consen  435 VPSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI-------KSHCYVSYSSVEEAAATREALHNVQWP  507 (718)
T ss_pred             CCCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHh-------hcceeEecccHHHHHHHHHHHhccccC
Confidence            34445667889999999988889999999998 5677777755333       56799999999999999999975332 


Q ss_pred             -ecCceEEEEEccccc
Q psy3345         754 -LYGRRLVLEWAEEAD  768 (787)
Q Consensus       754 -~~Gr~l~v~~A~~~~  768 (787)
                       -++++|.+.|+..++
T Consensus       508 ~sNPK~L~adf~~~de  523 (718)
T KOG2416|consen  508 PSNPKHLIADFVRADE  523 (718)
T ss_pred             CCCCceeEeeecchhH
Confidence             345999999998654

>KOG4849|consensus

Probab=95.87  E-value=0.0051  Score=61.79  Aligned_cols=75  Identities=9%  Similarity=0.221  Sum_probs=66.8

Q ss_pred             cccCCCccCCHHHHHHHhhccC--ceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEccC
Q psy3345          21 DEVEFIYKITQEQLKAKFEEKG--TVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        21 ~~~~lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~~   95 (787)
                      +|-||-|.+|.+||.+.....|  .+-++++.-++ +|+|+|||.|..-+....++-++.|-...|.|..=.|..+..
T Consensus        84 YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~NK  161 (498)
T KOG4849|consen   84 YVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYNK  161 (498)
T ss_pred             EecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccch
Confidence            3445999999999999999988  67889999888 899999999999999999999999999999998888877764

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.26  E-value=0.081  Score=47.70  Aligned_cols=56  Identities=16%  Similarity=0.291  Sum_probs=45.7

Q ss_pred             HHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCcc
Q psy3345         596 SIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN  665 (787)
Q Consensus       596 ~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~  665 (787)
                      +|.+.|..||.+.-+++.-             +.-+|.|.+...|.+|+. ++|..+.|+.|.|++..+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~-------------~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVG-------------DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEET-------------TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeC-------------CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            6778899999988887764             458999999999999999 9999999999999886543

; PDB: 1UFW_A 2DNR_A.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.14  E-value=0.072  Score=42.68  Aligned_cols=53  Identities=17%  Similarity=0.279  Sum_probs=44.6

Q ss_pred             ccceEEEeCCCCCCCHHhHHHhhcCCCCcceeecccceEEEeecChHhHHHHHh
Q psy3345         223 QYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALN  276 (787)
Q Consensus       223 ~~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~~~g~afV~F~~~~~A~~Al~  276 (787)
                      ..++.+|. .|......||.++|++||-+.|..+....|||...+.+.|..++.
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~dTSAfV~l~~r~~~~~v~~   60 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWINDTSAFVALHNRDQAKVVMN   60 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEEEEEECTTEEEEEECCCHHHHHHHH
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcCCcEEEEeecHHHHHHHHH
Confidence            45677777 999999999999999999999999988999999999999999888

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.99  E-value=0.12  Score=46.70  Aligned_cols=56  Identities=32%  Similarity=0.394  Sum_probs=45.0

Q ss_pred             HHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       352 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      +|.+.|..||.+.-++++-+        .-+|+|.+-+.|.+|++ ++|..++|+.|.|....+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            67778889999888877543        47999999999999997 9999999999999987764

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.96  E-value=0.11  Score=39.49  Aligned_cols=54  Identities=19%  Similarity=0.261  Sum_probs=44.1

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhc----CCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHh
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAF----GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL  748 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~----G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l  748 (787)
                      ...|+|+|+ .+++.+||+.+|..|    + ...|...-|.        .|-|.|.+.+.|.+||.+|
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt--------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEG-PFRIEWIDDT--------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCC-CceEEEecCC--------cEEEEECCHHHHHHHHHcC
Confidence            457999999 458888999999998    5 5567766662        4889999999999999865

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.57  E-value=0.16  Score=45.02  Aligned_cols=74  Identities=22%  Similarity=0.269  Sum_probs=56.7

Q ss_pred             CCCCCEEEEecCCcc----CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         682 KQTGSKILVRNIPFQ----AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~----~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      ..+..+|.|+=|+..    -+-+.+-...+.||.|.+|.+.-.        ..|.|.|.+..+|-+|+.++.  ...-|.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr--------qsavVvF~d~~SAC~Av~Af~--s~~pgt  152 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR--------QSAVVVFKDITSACKAVSAFQ--SRAPGT  152 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC--------ceEEEEehhhHHHHHHHHhhc--CCCCCc
Confidence            346677887655444    344456667789999999988544        369999999999999999994  466789


Q ss_pred             eEEEEEcc
Q psy3345         758 RLVLEWAE  765 (787)
Q Consensus       758 ~l~v~~A~  765 (787)
                      .+..+|-.
T Consensus       153 m~qCsWqq  160 (166)
T PF15023_consen  153 MFQCSWQQ  160 (166)
T ss_pred             eEEeeccc
Confidence            99998865

>KOG2416|consensus

Probab=94.51  E-value=0.032  Score=60.54  Aligned_cols=77  Identities=18%  Similarity=0.160  Sum_probs=63.0

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee---CCeEE
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFE-KYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF---LGRML  408 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~---~g~~l  408 (787)
                      ...++.|||.||-...|.-+|+.++. ..|.|.+.+|-.      -+..|||.|.+.++|.....+|||..+   +++.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            34567899999999999999999999 566677765522      334799999999999999999999865   66888


Q ss_pred             EEeeCCC
Q psy3345         409 HLIPGKP  415 (787)
Q Consensus       409 ~v~~~~~  415 (787)
                      .+.+...
T Consensus       515 ~adf~~~  521 (718)
T KOG2416|consen  515 IADFVRA  521 (718)
T ss_pred             Eeeecch
Confidence            8888664

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.16  E-value=0.066  Score=51.06  Aligned_cols=69  Identities=13%  Similarity=0.107  Sum_probs=46.6

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhc-cCce---EEEEEEecC--C-CCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEE-KGTV---TDVQLKYTT--E-GKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~-~g~i---~~~~~~~~~--~-g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ...+|+||.     ||+++||+++.+..+. ++.-   ..+.-.+..  . -....-|||.|.+.++...-.+.+||..|
T Consensus         6 ~~~KvVIR~-----LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen    6 EGTKVVIRR-----LPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             ---EEEEEE-----E-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred             cCceEEEeC-----CCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence            456899999     9999999999998887 6654   233322322  1 12346799999999999999999999654


Q ss_pred             C
Q psy3345          84 F   84 (787)
Q Consensus        84 ~   84 (787)
                      .
T Consensus        81 ~   81 (176)
T PF03467_consen   81 V   81 (176)
T ss_dssp             E
T ss_pred             E
Confidence            3

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.08  E-value=0.14  Score=38.93  Aligned_cols=51  Identities=22%  Similarity=0.307  Sum_probs=44.6

Q ss_pred             ceEEEeCCCCCCCHHhHHHhhcCC----CCcceeecccceEEEeecChHhHHHHHh
Q psy3345         225 HTIVVKNLPAGVKKKDLKAYFKPL----PLASVRTTFLGMAYIGFKDEKNCNKALN  276 (787)
Q Consensus       225 ~~v~v~nLp~~~te~di~~~F~~~----g~v~i~i~~~g~afV~F~~~~~A~~Al~  276 (787)
                      ..|+|+|+. +.+.+||..||..+    ++..|..+.-..|-|.|.+.+.|.+||.
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEETAARALV   60 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHHHHHHHH
Confidence            469999996 68889999999999    6667888877788999999999999986

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=93.89  E-value=0.28  Score=39.39  Aligned_cols=62  Identities=23%  Similarity=0.354  Sum_probs=45.8

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN   79 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~   79 (787)
                      .+|..++.+|+-..     .|..=...||.++|+.||.| .|.-+-+      .-|||.....++|..|+..++
T Consensus         2 ~d~~P~RdHVFhlt-----FPkeWK~~DI~qlFspfG~I-~VsWi~d------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    2 PDPQPSRDHVFHLT-----FPKEWKTSDIYQLFSPFGQI-YVSWIND------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             S----SGCCEEEEE-------TT--HHHHHHHCCCCCCE-EEEEECT------TEEEEEECCCHHHHHHHHHHT
T ss_pred             CCCCCCcceEEEEe-----CchHhhhhhHHHHhccCCcE-EEEEEcC------CcEEEEeecHHHHHHHHHHhc
Confidence            35677888999999     99999999999999999984 4555544      479999999999999999865

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.14  E-value=0.32  Score=43.13  Aligned_cols=74  Identities=15%  Similarity=0.136  Sum_probs=56.5

Q ss_pred             cCCCCEEEEeCCCCCC----CHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEec
Q psy3345         444 ARSKRIILVKNLPYRT----LPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  519 (787)
Q Consensus       444 ~~~~~~i~v~nlp~~~----t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  519 (787)
                      .++-.+|.|+=|...+    +...+....+.||+|.+|.+. ++..|.|.|.+..+|-+|+.+++. ...|..+.+.|..
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqq  160 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQ  160 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeeccc
Confidence            4456678886555544    445566678889999998754 556899999999999999999876 5667888888864

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=93.08  E-value=0.82  Score=39.64  Aligned_cols=74  Identities=14%  Similarity=0.077  Sum_probs=53.0

Q ss_pred             CCCCcccceEEEecCcccCCCc-cCCHHHHHHHhhcc-CceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIY-KITQEQLKAKFEEK-GTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~-~~~~~~l~~~f~~~-g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ..|...+..+.+..     .|. ..+-++|..+.+.+ ..|..++|+++. ..++=.+.++|.+.++|..-...+||+.+
T Consensus         6 ~~~~~~~~~~~~l~-----vp~~~~~~d~l~~f~~~~~~~i~~~riird~-~pnrymVLikF~~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen    6 DLPDERRSTLCCLA-----VPPYMTPSDFLLFFGAPFREDIEHIRIIRDG-TPNRYMVLIKFRDQESADEFYEEFNGKPF   79 (110)
T ss_pred             CCCCCCCceEEEEE-----eCcccccHHHHHHhhhcccccEEEEEEeeCC-CCceEEEEEEECCHHHHHHHHHHhCCCcc
Confidence            34455556666655     555 44556666665555 367788888763 23777899999999999999999999987


Q ss_pred             CC
Q psy3345          84 FS   85 (787)
Q Consensus        84 ~~   85 (787)
                      ..
T Consensus        80 ns   81 (110)
T PF07576_consen   80 NS   81 (110)
T ss_pred             CC
Confidence            54

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0804|consensus

Probab=92.26  E-value=0.43  Score=50.58  Aligned_cols=77  Identities=16%  Similarity=0.136  Sum_probs=63.2

Q ss_pred             CCCCCCCcc-cceEEEecCcccCCCccCCHHHHHHHhhccC-ceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345           3 NHLSGPVVP-RNHISLLDLDEVEFIYKITQEQLKAKFEEKG-TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus         3 ~~~~~~~~~-~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      +++|.+..+ +.-+.|..     .|..+|..||..|...+- .|.+++|++|..+ ++=.+.|+|.+.+||......|||
T Consensus        64 ~~~s~~~~~~~~mLcila-----VP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNG  137 (493)
T KOG0804|consen   64 SHSSLKNASSSTMLCILA-----VPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNG  137 (493)
T ss_pred             cccccccCCCCcEEEEEe-----ccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCC
Confidence            344444444 67789999     999999999999999885 7899999996332 455789999999999999999999


Q ss_pred             CccCC
Q psy3345          81 TYVFS   85 (787)
Q Consensus        81 ~~~~~   85 (787)
                      +.|..
T Consensus       138 k~Fn~  142 (493)
T KOG0804|consen  138 KQFNS  142 (493)
T ss_pred             CcCCC
Confidence            98754

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=92.22  E-value=0.19  Score=47.86  Aligned_cols=68  Identities=21%  Similarity=0.263  Sum_probs=44.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh-cCCe---eEEEEecCCCC-C-CcceEEEEEEcCHHHHHHHHHHhCCcee
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEK-YGPL---AEVILPIDKET-D-KTKGFALVTFLMPEHATQAYQHLDGTVF  403 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~-~G~i---~~v~i~~~~~~-~-~~~g~afV~F~~~~~A~~a~~~l~~~~~  403 (787)
                      ...|.||+||+.+|++++++.++. ++..   ..+.-...... + ....-|||.|.+.++...-...++|..+
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence            458999999999999999987776 5554   22321111111 1 1234699999999999999998998766

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2135|consensus

Probab=92.16  E-value=0.098  Score=55.46  Aligned_cols=66  Identities=17%  Similarity=0.252  Sum_probs=57.3

Q ss_pred             CCccC-CHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEccCC
Q psy3345          25 FIYKI-TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNL   96 (787)
Q Consensus        25 lp~~~-~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~~~   96 (787)
                      .|+.. |-.+|..||..||.|.+|.+-+.     ---|.|+|.+.-+|-+|..- ++..|++|.|.|++-.+-
T Consensus       380 ~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~s-~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  380 SPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYAS-HGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             cCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhcc-ccceecCceeEEEEecCC
Confidence            44444 66899999999999999998775     34799999999999999887 999999999999999873

>KOG4285|consensus

Probab=90.95  E-value=0.61  Score=46.73  Aligned_cols=69  Identities=14%  Similarity=0.162  Sum_probs=56.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCee-EEEEE
Q psy3345         447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVP-LYLEW  517 (787)
Q Consensus       447 ~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~-l~v~~  517 (787)
                      ..=|.|-++|.... .-|..+|++||.|.+.....++.+-+|.|.+.-+|.+|+. -+|+.|.|.. |-|..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKP  266 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeee
Confidence            45677888876543 4688899999999999988888999999999999999998 5888888754 34444

>KOG4285|consensus

Probab=90.83  E-value=0.41  Score=47.88  Aligned_cols=64  Identities=23%  Similarity=0.263  Sum_probs=52.1

Q ss_pred             CCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc-eEEEEEccC
Q psy3345          25 FIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS-RIKVEKCSN   95 (787)
Q Consensus        25 lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~-~i~v~~~~~   95 (787)
                      .|...+ .=|-.+|+.||+|.+....     +.-.+-+|.|.+.-+|++||.+ ||..|+|. .|-|..|..
T Consensus       205 Fppg~~-s~vL~~F~~cG~Vvkhv~~-----~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  205 FPPGQV-SIVLNLFSRCGEVVKHVTP-----SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cCccch-hHHHHHHHhhCeeeeeecC-----CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCC
Confidence            887554 4566889999998776444     3346999999999999999999 99999996 778988875

>KOG2591|consensus

Probab=90.62  E-value=0.79  Score=49.77  Aligned_cols=70  Identities=19%  Similarity=0.265  Sum_probs=55.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHhhcc--CCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcC--CeeCCeeEEEE
Q psy3345         446 SKRIILVKNLPYRTLPTDLKALFEP--FGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLE  516 (787)
Q Consensus       446 ~~~~i~v~nlp~~~t~~~l~~~F~~--~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~--~~~~g~~l~v~  516 (787)
                      ..+.|+++-||..+-.++++.+|+.  +-.+.+|.+..+.+ =||.|.+..||+.|.+.|..  +.|.|++|...
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            4578999999999999999999985  45566776655443 48999999999999998864  55777776543

>KOG2068|consensus

Probab=90.50  E-value=0.14  Score=52.42  Aligned_cols=84  Identities=12%  Similarity=0.268  Sum_probs=64.2

Q ss_pred             CCeEEecCCCCCCCHHHHH---HHHhhcCCeEEEEEeecCC-CCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCe
Q psy3345         580 DTTLYIKNLNFNSTEDSIR---RHFKKCGPIASVTVARKKD-PKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH  655 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~---~~F~~~G~v~~v~i~~~~~-~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~  655 (787)
                      ..-+||-+|++...++.+.   +.|.+||.|..+.+..+.. ....+   ...-++|.|...++|..||...+|..++|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~---~~~s~yITy~~~eda~rci~~v~g~~~dg~  153 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSG---GTCSVYITYEEEEDADRCIDDVDGFVDDGR  153 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCC---CCCcccccccchHhhhhHHHHhhhHHhhhh
Confidence            4567888899887766665   5789999999998887663 11111   112389999999999999999999999999


Q ss_pred             EEEEEecCccc
Q psy3345         656 QIELKRSNRNL  666 (787)
Q Consensus       656 ~l~v~~~~~~~  666 (787)
                      .|+..+...+.
T Consensus       154 ~lka~~gttky  164 (327)
T KOG2068|consen  154 ALKASLGTTKY  164 (327)
T ss_pred             hhHHhhCCCcc
Confidence            98877765543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=90.34  E-value=0.93  Score=35.14  Aligned_cols=55  Identities=16%  Similarity=0.335  Sum_probs=44.8

Q ss_pred             cCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        28 ~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      .++-+|++..+..|+- ++|.  .+++    || ||.|.+-.+|+++....|++.+-+.++.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I~--~d~t----Gf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRIR--DDRT----GF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceEE--ecCC----EE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4677999999999964 5554  4433    44 99999999999999999999988887765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=90.32  E-value=0.59  Score=44.71  Aligned_cols=61  Identities=15%  Similarity=0.097  Sum_probs=45.9

Q ss_pred             CHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc--cCccCCceEEEEEccC
Q psy3345          30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN--NTYVFSSRIKVEKCSN   95 (787)
Q Consensus        30 ~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~--~~~~~~~~i~v~~~~~   95 (787)
                      ..+.|+++|..++.+.....+..     -+-..|.|.+.++|.+|...|+  +..+.|..+.|.++.+
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            34789999999998777766643     5678999999999999999999  8999999999999965

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2068|consensus

Probab=90.03  E-value=0.14  Score=52.25  Aligned_cols=78  Identities=23%  Similarity=0.391  Sum_probs=61.6

Q ss_pred             eEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEecCCC----CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         338 RIFVRNLSYTVTEDDLT---KLFEKYGPLAEVILPIDKE----TDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~---~~F~~~G~i~~v~i~~~~~----~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      -+||-+||..+..+.+.   +.|.+||.|..|.+-.+..    .+.. .-+||+|...++|..||...+|..+.|+.++.
T Consensus        79 lvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   79 LVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            58888899887665554   4889999999998877652    1212 23899999999999999999999999999888


Q ss_pred             eeCCCC
Q psy3345         411 IPGKPK  416 (787)
Q Consensus       411 ~~~~~~  416 (787)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            776654

>KOG2591|consensus

Probab=89.42  E-value=0.72  Score=50.05  Aligned_cols=69  Identities=19%  Similarity=0.211  Sum_probs=56.1

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhcc--CceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc--CccCC
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEK--GTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN--TYVFS   85 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~--~~~~~   85 (787)
                      ..+--|+||-     +|-+.-.|+++.||++-  =.+.+|.+-.+      .-=||+|++..||+.|.++|.-  +.|+|
T Consensus       173 ~kRcIvilRE-----Ipettp~e~Vk~lf~~encPk~iscefa~N------~nWyITfesd~DAQqAykylreevk~fqg  241 (684)
T KOG2591|consen  173 HKRCIVILRE-----IPETTPIEVVKALFKGENCPKVISCEFAHN------DNWYITFESDTDAQQAYKYLREEVKTFQG  241 (684)
T ss_pred             cceeEEEEee-----cCCCChHHHHHHHhccCCCCCceeeeeeec------CceEEEeecchhHHHHHHHHHHHHHhhcC
Confidence            3344478888     99999999999999983  47789999886      2469999999999999999864  47888


Q ss_pred             ceEE
Q psy3345          86 SRIK   89 (787)
Q Consensus        86 ~~i~   89 (787)
                      +.|.
T Consensus       242 KpIm  245 (684)
T KOG2591|consen  242 KPIM  245 (684)
T ss_pred             cchh
Confidence            7664

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=88.96  E-value=1.6  Score=34.92  Aligned_cols=58  Identities=14%  Similarity=0.336  Sum_probs=38.0

Q ss_pred             cCCHHHHHHHhhccC-----ceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEc
Q psy3345          28 KITQEQLKAKFEEKG-----TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        28 ~~~~~~l~~~f~~~g-----~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      .++..+|..++...+     .|-+|.|.-+       |+||.-.. +.|..+++.|++..+.|++|.|+.|
T Consensus        12 g~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   12 GLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             T--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             CCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            567789999998884     4667887765       99999877 6899999999999999999999876

; PDB: 2G0C_A 3MOJ_B.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=88.57  E-value=1.6  Score=36.01  Aligned_cols=68  Identities=13%  Similarity=0.126  Sum_probs=45.5

Q ss_pred             EEEeecChHhHHHHHh--cCCcccCCeeEEEe--ecccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCC
Q psy3345         261 AYIGFKDEKNCNKALN--KNKSFWKGKQLNIY--KYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAES  336 (787)
Q Consensus       261 afV~F~~~~~A~~Al~--~~~~~l~g~~i~v~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  336 (787)
                      |+|+|..+.-|+.-++  .+...+++..+.|.  |+......                            .-........
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~----------------------------k~qv~~~vs~   52 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQ----------------------------KFQVFSGVSK   52 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCce----------------------------EEEEEEcccC
Confidence            7899999999999998  45666777666553  11110000                            0011223456


Q ss_pred             CeEEEcCCCCCCCHHHHHHH
Q psy3345         337 GRIFVRNLSYTVTEDDLTKL  356 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~  356 (787)
                      ++|.|.|||....+++|++.
T Consensus        53 rtVlvsgip~~l~ee~l~D~   72 (88)
T PF07292_consen   53 RTVLVSGIPDVLDEEELRDK   72 (88)
T ss_pred             CEEEEeCCCCCCChhhheee
Confidence            78999999999999999864

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=88.51  E-value=1.2  Score=42.62  Aligned_cols=62  Identities=18%  Similarity=0.051  Sum_probs=49.3

Q ss_pred             CHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhc--CCeeCCeeEEEEEecCc
Q psy3345         460 LPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA--YTKFKEVPLYLEWAPEG  521 (787)
Q Consensus       460 t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~--~~~~~g~~l~v~~~~~~  521 (787)
                      ..+.|+.+|..|+.+..+...++=+-..|.|.+.+.|.+|...|+  +..+.|..+.+.|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            457899999999999999988888899999999999999999999  99999999999988433

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2135|consensus

Probab=88.48  E-value=0.3  Score=51.95  Aligned_cols=73  Identities=23%  Similarity=0.396  Sum_probs=59.2

Q ss_pred             CeEEEcCCCCCC-CHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCC
Q psy3345         337 GRIFVRNLSYTV-TEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP  415 (787)
Q Consensus       337 ~~l~V~nLp~~~-te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  415 (787)
                      +.|-+.-.|+.. |..+|..+|.+||.|..|.+-..      .--|.|+|.+..+|-.|.. .++-.|++|.|+|.|.++
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            445566666664 56789999999999999988433      3369999999999988875 799999999999999886


Q ss_pred             C
Q psy3345         416 K  416 (787)
Q Consensus       416 ~  416 (787)
                      .
T Consensus       446 s  446 (526)
T KOG2135|consen  446 S  446 (526)
T ss_pred             C
Confidence            3

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=87.81  E-value=21  Score=36.23  Aligned_cols=188  Identities=13%  Similarity=0.172  Sum_probs=114.6

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCC--CCCCCCCCcccEEEEEeCCHHHHHHHH----HHhCC-
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD--PKSPGQFLSMGYGFVQFYTRESLNQAL----KVLQN-  649 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~--~~~~~~~~s~G~afV~F~~~e~A~~A~----~~lng-  649 (787)
                      ....+.|...|+..+++-..+...|-+||+|+++.++.+.+  .+............+.|-+.+.|..-.    +.|+. 
T Consensus        12 ~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEf   91 (309)
T PF10567_consen   12 EYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEF   91 (309)
T ss_pred             cceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHH
Confidence            34568899999999999999999999999999999998762  112222334567889999999875432    22322 


Q ss_pred             -CccCCeEEEEEecCccccchh--------h----hhhhccccccCCCCCEEEEecCCccCcHHH-HHHHH---HhcC--
Q psy3345         650 -SSLDEHQIELKRSNRNLESEA--------T----TVKRKSSNVAKQTGSKILVRNIPFQAKQSE-VEELF---KAFG--  710 (787)
Q Consensus       650 -~~l~g~~l~v~~~~~~~~~~~--------~----~~~~~~~~~~~~~~~~l~V~nLp~~~t~~d-L~~~F---~~~G--  710 (787)
                       ..+....|.+.|..-......        .    ...-..........+.|.|.=- ..+..++ +.+.+   ..=+  
T Consensus        92 K~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~-~~~~~~dl~~~kL~fL~~~~n~  170 (309)
T PF10567_consen   92 KTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFK-DPVDKDDLIEKKLPFLKNSNNK  170 (309)
T ss_pred             HHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEec-CccchhHHHHHhhhhhccCCCc
Confidence             445666777766542111000        0    0001111223345677777533 3333333 22222   1113  


Q ss_pred             --CeeEEEecccc-CCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec--CceEEEEEcc
Q psy3345         711 --ELKFVRLPKKM-VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY--GRRLVLEWAE  765 (787)
Q Consensus       711 --~I~~v~i~~~~-~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~--Gr~l~v~~A~  765 (787)
                        .|++|.|+.-- ....-+..||.+.|-+...|...+..+.....-.  .+...|+.+.
T Consensus       171 RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs~~~  230 (309)
T PF10567_consen  171 RYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVSVQP  230 (309)
T ss_pred             eEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEeccC
Confidence              25777775431 1234567799999999999999999886322222  4788888775

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=86.17  E-value=6.8  Score=34.03  Aligned_cols=67  Identities=12%  Similarity=0.108  Sum_probs=48.8

Q ss_pred             CeEEecCCCCC-CCHHHHHHHHhhcC-CeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy3345         581 TTLYIKNLNFN-STEDSIRRHFKKCG-PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDE  654 (787)
Q Consensus       581 ~~l~V~NLp~~-~t~~~L~~~F~~~G-~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g  654 (787)
                      ..+.+--.|+. ++.++|..+.+.+- .|..++|.++..       .++-.+.+.|.+.++|..-...+||+.+..
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-------pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-------PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-------CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            44444445555 55566665555543 478899988764       366788999999999999999999988743

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0804|consensus

Probab=85.36  E-value=4.3  Score=43.33  Aligned_cols=68  Identities=12%  Similarity=0.136  Sum_probs=58.8

Q ss_pred             CCeEEecCCCCCCCHHHHHHHHhhcC-CeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy3345         580 DTTLYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDE  654 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~~~F~~~G-~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g  654 (787)
                      .+.|+|--+|-.++..+|..+...+- .|.++++++|..       .++-...|.|.+.++|..-...+||+.+..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~-------pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM-------PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC-------CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            78999999999999999999988754 589999999765       245578999999999999999999988854

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=84.13  E-value=1.7  Score=35.89  Aligned_cols=71  Identities=24%  Similarity=0.255  Sum_probs=46.3

Q ss_pred             EEEEEcCHHHHHHHHHHhCC-ceeCCeEEEEe--eCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCC
Q psy3345         381 ALVTFLMPEHATQAYQHLDG-TVFLGRMLHLI--PGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY  457 (787)
Q Consensus       381 afV~F~~~~~A~~a~~~l~~-~~~~g~~l~v~--~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~  457 (787)
                      |.|+|....-|++.++.-.. ..+++..+.|.  +.......                 .+ +.....+.++|+|.|||.
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~-----------------k~-qv~~~vs~rtVlvsgip~   62 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQ-----------------KF-QVFSGVSKRTVLVSGIPD   62 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCce-----------------EE-EEEEcccCCEEEEeCCCC
Confidence            68999999999999973221 24555555543  33321000                 00 122345678999999999


Q ss_pred             CCCHHHHHHhhc
Q psy3345         458 RTLPTDLKALFE  469 (787)
Q Consensus       458 ~~t~~~l~~~F~  469 (787)
                      ...+++|++...
T Consensus        63 ~l~ee~l~D~Le   74 (88)
T PF07292_consen   63 VLDEEELRDKLE   74 (88)
T ss_pred             CCChhhheeeEE
Confidence            999999998654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG4574|consensus

Probab=84.10  E-value=0.69  Score=52.80  Aligned_cols=74  Identities=18%  Similarity=0.236  Sum_probs=63.3

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee--cCceEEEEEc
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL--YGRRLVLEWA  764 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~--~Gr~l~v~~A  764 (787)
                      +.++.|.+-..+-.-|-.+|+.||.|.+.+.+++.       ..|.|+|.+.+.|..|+.+|. |+.+  -|-+.+|.||
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~-------N~alvs~~s~~sai~a~dAl~-gkevs~~g~Ps~V~~a  371 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL-------NMALVSFSSVESAILALDALQ-GKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc-------cchhhhhHHHHHHHHhhhhhc-CCcccccCCceeEEec
Confidence            35578888889999999999999999999998884       479999999999999999996 5644  4889999999


Q ss_pred             cccc
Q psy3345         765 EEAD  768 (787)
Q Consensus       765 ~~~~  768 (787)
                      +.-.
T Consensus       372 k~~~  375 (1007)
T KOG4574|consen  372 KTLP  375 (1007)
T ss_pred             cccc
Confidence            8543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=83.39  E-value=4.9  Score=31.20  Aligned_cols=56  Identities=18%  Similarity=0.310  Sum_probs=44.3

Q ss_pred             cCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         696 QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       696 ~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .++-.|++..+..|+ ...|+.  +.      .| -||.|.+..+|.++....+ ++.+.+.+|.++
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~~--d~------tG-fYIvF~~~~Ea~rC~~~~~-~~~~f~y~m~M~   66 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIRD--DR------TG-FYIVFNDSKEAERCFRAED-GTLFFTYRMQME   66 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEEe--cC------CE-EEEEECChHHHHHHHHhcC-CCEEEEEEEEeC
Confidence            468899999999998 544543  31      34 4899999999999999986 799998888763

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=82.91  E-value=0.81  Score=42.63  Aligned_cols=106  Identities=15%  Similarity=0.089  Sum_probs=71.6

Q ss_pred             CCHHhHHHhhcC----CCCcceeecccceEEEeecChHhHHHHHhcCCcccCCeeEEEeecccCCccccCCCcCCCCchh
Q psy3345         236 VKKKDLKAYFKP----LPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNAS  311 (787)
Q Consensus       236 ~te~di~~~F~~----~g~v~i~i~~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~  311 (787)
                      .+-..|...+..    .+.+.++-+..+...+.|.+++++.+++....-.+.|..+.+.+|.+...+..           
T Consensus        29 ~~~~~l~~~l~~~W~~~~~~~i~~l~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~~~~~~-----------   97 (153)
T PF14111_consen   29 ISLSALEQELAKIWKLKGGVKIRDLGDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPDFNPSE-----------   97 (153)
T ss_pred             CCHHHHHHHHHHHhCCCCcEEEEEeCCCeEEEEEEeccceeEEEecccccccccchhhhhhcccccccc-----------
Confidence            445555555544    34445555588899999999999999999777777888888764432211100           


Q ss_pred             hhhhhhcccccccchhhhhcccCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEec
Q psy3345         312 MENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYT-VTEDDLTKLFEKYGPLAEVILPI  370 (787)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~i~~  370 (787)
                                        ........-|.|.|||.. .+++-++.+-+.+|.+..+....
T Consensus        98 ------------------~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t  139 (153)
T PF14111_consen   98 ------------------VKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENT  139 (153)
T ss_pred             ------------------cceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCC
Confidence                              000011235788899998 67778888999999999887643

>KOG4574|consensus

Probab=82.46  E-value=0.94  Score=51.76  Aligned_cols=78  Identities=17%  Similarity=0.145  Sum_probs=64.9

Q ss_pred             EEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeC--CeeEEEEEecCccccccc
Q psy3345         450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK--EVPLYLEWAPEGVFAEAK  527 (787)
Q Consensus       450 i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~--g~~l~v~~~~~~~~~~~~  527 (787)
                      ..+.|.+-..+..-|..+|+.||.|.+....++-..|.|+|.+.+.|..|+.+|+|+.+.  |-+.+|.++..-.|..++
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~~ep~  380 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPMYEPP  380 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccccccCC
Confidence            334455666778889999999999999999888899999999999999999999998865  889999988665444433

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=81.11  E-value=4.2  Score=32.49  Aligned_cols=59  Identities=17%  Similarity=0.244  Sum_probs=36.4

Q ss_pred             ccCcHHHHHHHHHhcCC-----eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         695 FQAKQSEVEELFKAFGE-----LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       695 ~~~t~~dL~~~F~~~G~-----I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      ..++..+|..++..-+.     |-.++|..+         |+||+-.. +.|..+++.|+ +..+.|++|.|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~---------~S~vev~~-~~a~~v~~~l~-~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN---------FSFVEVPE-EVAEKVLEALN-GKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS----------EEEEE-T-T-HHHHHHHHT-T--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee---------EEEEEECH-HHHHHHHHHhc-CCCCCCeeEEEEEC
Confidence            45788899988886644     455777555         79999877 47999999997 69999999999876

; PDB: 2G0C_A 3MOJ_B.

>KOG2253|consensus

Probab=81.00  E-value=1  Score=50.17  Aligned_cols=156  Identities=12%  Similarity=0.191  Sum_probs=97.0

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      ..+..++||+|+...+..+-+..+...||.|.++....              |||+.|..+..+.+|+..++-..++|..
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------------fgf~~f~~~~~~~ra~r~~t~~~~~~~k  102 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------------FGFCEFLKHIGDLRASRLLTELNIDDQK  102 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------------hcccchhhHHHHHHHHHHhcccCCCcch
Confidence            45567999999999999999999999999998887653              9999999999999999999999999988


Q ss_pred             EEEEecCccccchhh----hhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEE
Q psy3345         657 IELKRSNRNLESEAT----TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF  732 (787)
Q Consensus       657 l~v~~~~~~~~~~~~----~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~af  732 (787)
                      +.+..-.........    .......-.+....+-..+.|+|...........+.--+...+.+-....  .+....++|
T Consensus       103 l~~~~d~q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is~s~~s~~~~~e~--d~h~~e~~~  180 (668)
T KOG2253|consen  103 LIENVDEQTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQISSSAASRRQIAEA--DDHCLELEK  180 (668)
T ss_pred             hhccchhhhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHhccchhhhhhhhHHH--HHHHHHHHH
Confidence            877653221111000    00000000111114556678888877776666666544433333332221  222333444


Q ss_pred             EEecCHHHHHHHHHHh
Q psy3345         733 VEFITKNEAKRAMKAL  748 (787)
Q Consensus       733 V~F~~~~~A~~Al~~l  748 (787)
                      -.|.+...+..+....
T Consensus       181 ~~~~s~~~~~~~~~~~  196 (668)
T KOG2253|consen  181 TETESNSALSKEAESK  196 (668)
T ss_pred             hhcccccccCcccccc
Confidence            4444444444444333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	787
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		5e-34
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-23
1whx_A	111	Solution Structure Of The Second Rna Binding Domain		1e-19
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		1e-13
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		6e-10
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-09
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-09
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		3e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-09
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-08
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-08
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-04
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		5e-08
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		8e-08
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-07
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		1e-07
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		3e-07
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		3e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-07
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		6e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		8e-06
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		1e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-06
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		5e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		5e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		6e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-06
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		9e-06
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		3e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-05
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		3e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		4e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		6e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-04
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		1e-04
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		1e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		2e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		2e-04
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		2e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-04
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		3e-04
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		3e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		3e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		3e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		3e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		3e-04
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		4e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		5e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		5e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		5e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		7e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		7e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		9e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-04

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score =  142 bits (359), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 66/91 (72%), Positives = 73/91 (80%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
           KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +A
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 742 KRAMKALCQSTHLYGRRLVLEWAEEADNVED 772
           K+A  ALC STHLYGRRLVLEWA+    V+ 
Sbjct: 72  KKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/75 (64%), Positives = 58/75 (77%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FVRNLSYT +E+DL KLF  YGPL+E+  PID  T K KGFA VTF+ PEHA +AY  
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 398 LDGTVFLGRMLHLIP 412
           +DG VF GRMLH++P
Sbjct: 70  VDGQVFQGRMLHVLP 84

>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From Hypothetical Protein Bab23448 Length = 111

Iteration: 1
 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 55/77 (71%)
Query: 447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 506
           K +IL KNLP  TL  +++  F  FG LGRVL+P  GIT +VEFL+  +A+ AF  LAY+
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 507 KFKEVPLYLEWAPEGVF 523
           KF  VPLYLEWAP GVF
Sbjct: 70  KFHHVPLYLEWAPIGVF 86

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 75.5 bits (184), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/85 (42%), Positives = 58/85 (68%), Gaps = 2/85 (2%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
            + L+IKNLNF++TE++++  F K G I S T+++KK+    G  LSMG+GFV++   E 
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNK--AGVLLSMGFGFVEYKKPEQ 62
Query: 640 LNQALKVLQNSSLDEHQIELKRSNR 664
             +ALK LQ  ++D H++E++ S R
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISER 87

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 53/201 (26%), Positives = 88/201 (43%), Gaps = 58/201 (28%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ NL+   TED ++++F+  GPIA++ +   K+ K      ++ Y FV+++     N 
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK------NVNYAFVEYHQSHDANI 56
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
           AL+ L                                  KQ  + I+  N  FQ++QS  
Sbjct: 57  ALQTLN--------------------------------GKQIENNIVKINWAFQSQQSSS 84
Query: 703 EELFKAF-GELK-----------FVRLPKKMVG-------SGLHRGFGFVEFITKNEAKR 743
           ++ F  F G+L            F   P  + G       +G  RG+GFV F ++++A+ 
Sbjct: 85  DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 744 AMKALCQSTHLYGRRLVLEWA 764
           AM ++ Q   L GR L + WA
Sbjct: 145 AMDSM-QGQDLNGRPLRINWA 164

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T++S+R HF++ G +    V R  DP +     S G+GFV + T E ++ 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 63
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
           A+   +   +D   +E KR+          V R+ S    A  T  KI V  I    ++ 
Sbjct: 64  AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 112
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
            + + F+ +G+++ + +     GSG  RGF FV F
Sbjct: 113 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 146

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T++S+R HF++ G +    V R  DP +     S G+GFV + T E ++ 
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 68
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
           A+   +   +D   +E KR+          V R+ S    A  T  KI V  I    ++ 
Sbjct: 69  AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 117
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
            + + F+ +G+++ + +     GSG  RGF FV F
Sbjct: 118 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 151

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T++S+R HF++ G +    V R  DP +     S G+GFV + T E ++ 
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 70
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
           A+   +   +D   +E KR+          V R+ S    A  T  KI V  I    ++ 
Sbjct: 71  AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
            + + F+ +G+++ + +     GSG  RGF FV F
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 153

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T++S+R HF++ G +    V R  DP +     S G+GFV + T E ++ 
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 70
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
           A+   +   +D   +E KR+          V R+ S    A  T  KI V  I    ++ 
Sbjct: 71  AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
            + + F+ +G+++ + +     GSG  RGF FV F
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 153

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T++S+R HF++ G +    V R  DP +     S G+GFV + T E ++ 
Sbjct: 15  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 69
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
           A+   +   +D   +E KR+          V R+ S    A  T  KI V  I    ++ 
Sbjct: 70  AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 118
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
            + + F+ +G+++ + +     GSG  RGF FV F
Sbjct: 119 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 152

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L+F +T++S+R HF++ G +    V R  DP +     S G+GFV + T E ++ 
Sbjct: 17  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 71
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
           A+   +   +D   +E KR+          V R+ S    A  T  KI V  I    ++ 
Sbjct: 72  AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 120
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
            + + F+ +G+++ + +     GSG  RGF FV F
Sbjct: 121 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 154

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 74/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  N T+D +R  F   G + S  + R K         S+GYGFV + T +  
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH-----SLGYGFVNYVTAKDA 57
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
            +A+  L    L    I++            +  R SS V K   + + +  +P    Q 
Sbjct: 58  ERAINTLNGLRLQSKTIKV------------SYARPSSEVIKD--ANLYISGLPRTMTQK 103
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           +VE++F  FG +   R+      +GL RG  F+ F  ++EA+ A+ + 
Sbjct: 104 DVEDMFSRFGRIINSRVLVDQT-TGLSRGVAFIRFDKRSEAEEAITSF 150

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 74/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  N T+D +R  F   G + S  + R K         S+GYGFV + T +  
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH-----SLGYGFVNYVTAKDA 57
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
            +A+  L    L    I++            +  R SS V K   + + +  +P    Q 
Sbjct: 58  ERAINTLNGLRLQSKTIKV------------SYARPSSEVIKD--ANLYISGLPRTMTQK 103
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           +VE++F  FG +   R+      +GL RG  F+ F  ++EA+ A+ + 
Sbjct: 104 DVEDMFSRFGRIINSRVLVDQT-TGLSRGVAFIRFDKRSEAEEAITSF 150

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I+V NL Y+ T + + +LF ++G +  V L  D+ET K KGF  V  +  E  ++A   L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 399 DGTVFLGRMLHLIPGKPKEN 418
           D T F+GR + +    PK++
Sbjct: 63  DNTDFMGRTIRVTEANPKKS 82

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/168 (29%), Positives = 75/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  N T++  R  F   G I S  + R K     GQ  S+GYGFV +   +  
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK---ITGQ--SLGYGFVNYIDPKDA 57
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
            +A+  L    L    I++            +  R SS  A    + + V  +P    Q 
Sbjct: 58  EKAINTLNGLRLQTKTIKV------------SYARPSS--ASIRDANLYVSGLPKTMTQK 103
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           E+E+LF  +G +   R+    V +G+ RG GF+ F  + EA+ A+K L
Sbjct: 104 ELEQLFSQYGRIITSRILVDQV-TGVSRGVGFIRFDKRIEAEEAIKGL 150

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 48/168 (28%), Positives = 74/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  N T+D  +  F   G I S  + R K     GQ  S+GYGFV +      
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDK---ITGQ--SLGYGFVNYSDPNDA 59
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
           ++A+  L    L    I++            +  R SS  A    + + V  +P    Q 
Sbjct: 60  DKAINTLNGLKLQTKTIKV------------SYARPSS--ASIRDANLYVSGLPKTMSQK 105
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           E+E+LF  +G +   R+      +G+ RG GF+ F  + EA+ A+K L
Sbjct: 106 EMEQLFSQYGRIITSRILLDQA-TGVSRGVGFIRFDKRIEAEEAIKGL 152

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 29/86 (33%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           ++ G++FV  LS+   E  L ++F KYG ++EV++  D+ET +++GF  VTF   + A  
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 394 AYQHLDGTVFLGRMLHL-IPGKPKEN 418
           A   ++G    GR + +   GK  +N
Sbjct: 70  AMMAMNGKSVDGRQIRVDQAGKSSDN 95

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/88 (25%), Positives = 47/88 (53%), Gaps = 5/88 (5%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++  L+F++ E S+ + F K G I+ V V + ++ +      S G+GFV F   +    
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQR-----SRGFGFVTFENIDDAKD 69
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEA 670
           A+  +   S+D  QI + ++ ++ ++ +
Sbjct: 70  AMMAMNGKSVDGRQIRVDQAGKSSDNRS 97

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 41/70 (58%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V NL+Y  + D L ++FEKYG + +V +P D+ T +++GFA V F     A  A   +DG
Sbjct: 52  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 401 TVFLGRMLHL 410
            V  GR L +
Sbjct: 112 AVLDGRELRV 121

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 7/90 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T+L + NL + ++ D++RR F+K G +  V + R +  K      S G+ FV+F+ +   
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE-----SRGFAFVRFHDKRDA 102
Query: 641 NQALKVLQNSSLD--EHQIELKRSNRNLES 668
             A+  +  + LD  E ++++ R  R  +S
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYGRPPDS 132

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 55.8 bits (133), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 21/177 (11%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++  +    +E  +R  F++ G +  + V R +    P    S G  FV FYTR++  +
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTRKAALE 74
Query: 643 ALKVLQNSSL---DEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
           A   L N  +     H I++K ++            K++ V  +   K+ +  I  +  +
Sbjct: 75  AQNALHNMKVLPGMHHPIQMKPAD----------SEKNNAVEDR---KLFIGMISKKCTE 121
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
           +++  +F +FG+++  R+ +     GL RG  FV F T+  A+ A+KA+ Q+  + G
Sbjct: 122 NDIRVMFSSFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 176

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 69/137 (50%), Gaps = 14/137 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R++V ++ Y + ED + + F  +GP+  + +  D  T K KGFA V + +PE A  A + 
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
           ++  +  GR + +  G+P  N G          ++  +D   +  EAR+   I V ++  
Sbjct: 75  MNSVMLGGRNIKV--GRPS-NIGQ---------AQPIIDQLAE--EARAFNRIYVASVHQ 120
Query: 458 RTLPTDLKALFEPFGDL 474
                D+K++FE FG +
Sbjct: 121 DLSDDDIKSVFEAFGKI 137

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/169 (21%), Positives = 85/169 (50%), Gaps = 15/169 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM---GYGFVQFYTRES 639
           +Y+ ++ +   ED+IR+ F   GPI S+ ++           ++M   G+ FV++   E+
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS--------VTMKHKGFAFVEYEVPEA 67
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
              AL+ + +  L    I++ R + N+      + + +     +  ++I V ++      
Sbjct: 68  AQLALEQMNSVMLGGRNIKVGRPS-NIGQAQPIIDQLAEEA--RAFNRIYVASVHQDLSD 124
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
            +++ +F+AFG++K   L +    +G H+G+GF+E+     ++ A+ ++
Sbjct: 125 DDIKSVFEAFGKIKSCTLARDPT-TGKHKGYGFIEYEKAQSSQDAVSSM 172

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
           D+     + V NL+Y  + D L ++FEKYG + +V +P D+ T +++GFA V F     A
Sbjct: 66  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 392 TQAYQHLDGTVFLGRMLHL 410
             A   +DG V  GR L +
Sbjct: 126 EDAMDAMDGAVLDGRELRV 144

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 7/90 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T+L + NL + ++ D++RR F+K G +  V + R +  K      S G+ FV+F+ +   
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE-----SRGFAFVRFHDKRDA 125
Query: 641 NQALKVLQNSSLD--EHQIELKRSNRNLES 668
             A+  +  + LD  E ++++ R  R  +S
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYGRPPDS 155

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 21/177 (11%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++  +    +E  +R  F++ G +  + V R +    P    S G  FV FYTR++  +
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTRKAALE 62
Query: 643 ALKVLQNSSL---DEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
           A   L N  +     H I++K ++            K++ V  +   K+ +  I  +  +
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPAD----------SEKNNAVEDR---KLFIGMISKKCTE 109
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
           +++  +F +FG+++  R+ +     GL RG  FV F T+  A+ A+KA+ Q+  + G
Sbjct: 110 NDIRVMFSSFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 164

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/177 (24%), Positives = 84/177 (47%), Gaps = 20/177 (11%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           +A   R++V ++ Y + ED + + F  +GP+  + +  D  T K KGFA V + +PE A 
Sbjct: 25  LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84
Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILV 452
            A + ++  +  GR + +  G+P  N G          ++  +D   +  EAR+   I V
Sbjct: 85  LALEQMNSVMLGGRNIKV--GRP-SNIGQ---------AQPIIDQLAE--EARAFNRIYV 130
Query: 453 KNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
            ++       D+K++FE FG +    +     T      G +E+ +   ++ A +S+
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 83/168 (49%), Gaps = 9/168 (5%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           + +Y+ ++ +   ED+IR+ F   GPI S+ ++              G+ FV++   E+ 
Sbjct: 29  SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK-----HKGFAFVEYEVPEAA 83
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
             AL+ + +  L    I++ R + N+      + + +     +  ++I V ++       
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPS-NIGQAQPIIDQLAEEA--RAFNRIYVASVHQDLSDD 140
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           +++ +F+AFG++K   L +    +G H+G+GF+E+     ++ A+ ++
Sbjct: 141 DIKSVFEAFGKIKSATLARDPT-TGKHKGYGFIEYEKAQSSQDAVSSM 187

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 43/70 (61%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL +++T +DL ++F KYG + +V +  DK+T K+KG A + FL  + A    + +
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 399 DGTVFLGRML 408
           +     GR++
Sbjct: 79  NNKQLFGRVI 88

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/69 (36%), Positives = 42/69 (60%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R++V +L + +TED L  +FE +G +  + L +D ET ++KG+  +TF   E A +A + 
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 398 LDGTVFLGR 406
           L+G    GR
Sbjct: 88  LNGFELAGR 96

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 39/72 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV N+ Y  TE+ L  +F + GP+    L  D+ET K KG+    +   E A  A ++L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 399 DGTVFLGRMLHL 410
           +G  F GR L +
Sbjct: 71  NGREFSGRALRV 82

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           G++F+  L+    E  L  +F K+GP++EV+L I   T K++GFA +TF  P  A  A +
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLL-IKDRTSKSRGFAFITFENPADAKNAAK 66
Query: 397 HLDGTVFLGRMLHL 410
            ++G    G+ + +
Sbjct: 67  DMNGKSLHGKAIKV 80

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/169 (28%), Positives = 77/169 (45%), Gaps = 26/169 (15%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++I  LN+++TED++R +F K G     TV   K  K P    S G+GF+ F    S+++
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYG-----TVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
            +K      LD   I+ KR+    E + T               KI V  I    +  E 
Sbjct: 61  VVKT--QHILDGKVIDPKRAIPRDEQDKT--------------GKIFVGGIGPDVRPKEF 104
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS 751
           EE F  +G +   +L      +G  RGFGFV +    ++  A+  +CQ+
Sbjct: 105 EEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVTY----DSADAVDRVCQN 148

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 53.1 bits (126), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 66/137 (48%), Gaps = 14/137 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R++V ++ Y + ED + + F  +GP+  +    D  T K KGFA V + +PE A  A + 
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
            +     GR + +  G+P  N G          ++  +D   +  EAR+   I V ++  
Sbjct: 74  XNSVXLGGRNIKV--GRPS-NIGQ---------AQPIIDQLAE--EARAFNRIYVASVHQ 119
Query: 458 RTLPTDLKALFEPFGDL 474
                D+K++FE FG +
Sbjct: 120 DLSDDDIKSVFEAFGKI 136

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 35/165 (21%), Positives = 79/165 (47%), Gaps = 9/165 (5%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y+ ++ +   ED+IR+ F   GPI S+  +              G+ FV++   E+   
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXK-----HKGFAFVEYEVPEAAQL 69
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
           AL+   +  L    I++ R + N+      + + +     +  ++I V ++       ++
Sbjct: 70  ALEQXNSVXLGGRNIKVGRPS-NIGQAQPIIDQLAEEA--RAFNRIYVASVHQDLSDDDI 126
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + +F+AFG++K   L +    +G H+G+GF+E+     ++ A+ +
Sbjct: 127 KSVFEAFGKIKSCTLARDPT-TGKHKGYGFIEYEKAQSSQDAVSS 170

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S  ++V +L + +TED L  +FE +G +  ++L  D +T ++KG+  +TF   E A +A 
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 396 QHLDGTVFLGRMLHL 410
           + L+G    GR + +
Sbjct: 65  EQLNGFELAGRPMRV 79

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/90 (33%), Positives = 47/90 (52%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++  I V NLS    E DL +LF  +G ++ + L  DK T ++KGFA ++F   E A +A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDG 424
              + G  +   +L++   KP  N G   G
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/168 (23%), Positives = 72/168 (42%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
            +LY+ +L+ + TE  +   F   GPI S+ V R    +      S+GY +V F      
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR-----SLGYAYVNFQQPADA 70
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
            +AL  +    +    + +  S R+             ++ K     I ++N+       
Sbjct: 71  ERALDTMNFDVIKGKPVRIMWSQRD------------PSLRKSGVGNIFIKNLDKSIDNK 118
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
            + + F AFG +   ++     GS   +G+GFV F T+  A+RA++ +
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERAIEKM 163

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 77/167 (46%), Gaps = 21/167 (12%)
Query: 593 TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL 652
           +E  +R  F++ G +  + V R +    P    S G  FV FYTR++  +A   L N  +
Sbjct: 16  SEKDLRELFEQYGAVYEINVLRDRSQNPP---QSKGCCFVTFYTRKAALEAQNALHNXKV 72
Query: 653 ---DEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAF 709
                H I+ K ++            K++ V  +   K+ +  I  +  ++++   F +F
Sbjct: 73  LPGXHHPIQXKPAD----------SEKNNAVEDR---KLFIGXISKKCTENDIRVXFSSF 119
Query: 710 GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
           G+++  R+ +     GL RG  FV F T+  A+ A+KA  Q+    G
Sbjct: 120 GQIEECRILRGP--DGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEG 164

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A +  +G
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 401 TVFLGRMLHL 410
               GR + +
Sbjct: 111 MELDGRRIRV 120

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A +  +G
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 401 TVFLGRMLHL 410
               GR + +
Sbjct: 80  MELDGRRIRV 89

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 39/168 (23%), Positives = 72/168 (42%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
            +LY+ +L+ + TE  +   F   GPI S+ V R    +      S+GY +V F      
Sbjct: 11  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR-----SLGYAYVNFQQPADA 65
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
            +AL  +    +    + +  S R+             ++ K     I ++N+       
Sbjct: 66  ERALDTMNFDVIKGKPVRIMWSQRD------------PSLRKSGVGNIFIKNLDKSIDNK 113
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
            + + F AFG +   ++     GS   +G+GFV F T+  A+RA++ +
Sbjct: 114 ALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERAIEKM 158

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A +  +G
Sbjct: 17  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 401 TVFLGRMLHL 410
               GR + +
Sbjct: 77  MELDGRRIRV 86

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A +  +G
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 401 TVFLGRMLHL 410
               GR + +
Sbjct: 80  MELDGRRIRV 89

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 37/70 (52%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           V NL+Y  + D L ++FEKYG + +V +P +  T   +GFA V F     A  A   +DG
Sbjct: 18  VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 401 TVFLGRMLHL 410
               GR L +
Sbjct: 78  AELDGRELRV 87

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 7/85 (8%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TL + NL + ++ DS+RR F+K G +  V + R+   K+P      G+ FV+F+ R    
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAP-----RGFAFVRFHDRRDAQ 69
Query: 642 QALKVLQNSSLD--EHQIELKRSNR 664
            A   +  + LD  E ++++ R  R
Sbjct: 70  DAEAAMDGAELDGRELRVQVARYGR 94

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 86/194 (44%), Gaps = 21/194 (10%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMG----YGFVQFYTRE 638
           LY+ N+ F  TE+++   F     +  +T A    P +P   + +     + F++F + +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----PGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 639 SLNQALK----VLQNSSLDEHQIELKRSNRNL----ESEATTVKRKSSNVAKQTGSKILV 690
              QA+     + Q  SL   +I      + L    E+ +  V    S V   +  K+ +
Sbjct: 63  ETTQAMAFDGIIFQGQSL---KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 691 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ 750
             +P      +V+EL  +FG LK   L K    +GL +G+ F E++  N   +A+  L  
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGL-N 177
Query: 751 STHLYGRRLVLEWA 764
              L  ++L+++ A
Sbjct: 178 GMQLGDKKLLVQRA 191

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 39/72 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + V  +  TV E  L +LFE+YGP+  V +  D+ET +++G+  V F     A QA   L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 399 DGTVFLGRMLHL 410
           +G   L + L +
Sbjct: 105 NGFNILNKRLKV 116

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  ++Y  TE  L + FE YGP+  + +   K + K +G+A + +        AY+H 
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 399 DGTVFLGRML 408
           DG    GR +
Sbjct: 165 DGKKIDGRRV 174

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  ++Y  TE  L + FE YGP+  + +   K + K +G+A + +        AY+H 
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 399 DGTVFLGRML 408
           DG    GR +
Sbjct: 165 DGKKIDGRRV 174

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 23/77 (29%), Positives = 42/77 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A  A  ++
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 399 DGTVFLGRMLHLIPGKP 415
           + +   GR + +   KP
Sbjct: 75  NESELFGRTIRVNLAKP 91

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+FV NL   +TE+D  +LFE+YG  +EV +      ++ +GF  +       A  A   
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 398 LDGTVFLGRMLHL 410
           LDGT+   R L +
Sbjct: 78  LDGTILKSRPLRI 90

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV +LS  +T +D+   F  +G +++  +  D  T K+KG+  V+F     A  A Q +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 399 DGTVFLGRML 408
            G    GR +
Sbjct: 78  GGQWLGGRQI 87

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 49/103 (47%), Gaps = 14/103 (13%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYG----------PLAEVILPIDKETDKTKGFALV 383
           +++  I+V+ L+ +VT DDL   F++ G          P+  + L  DKET K KG A V
Sbjct: 13  SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL--DKETGKPKGDATV 70
Query: 384 TFLMPEHATQAYQHLDGTVFLGRML--HLIPGKPKENEGNVDG 424
           ++  P  A  A +  DG  F G  L   L   KP  N G   G
Sbjct: 71  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TLY+ NL+F +TE+ I   F K G I  + +   K  K+     + G+ FV++Y+R    
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKT-----ACGFCFVEYYSRADAE 95
Query: 642 QALKVLQNSSLDEHQI 657
            A++ +  + LD+  I
Sbjct: 96  NAMRYINGTRLDDRII 111

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G+ ++V  +P    Q E+  LF + GE++  +L +  V +G   G+GFV ++T  +A+RA
Sbjct: 19  GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAERA 77
Query: 745 MKAL 748
           +  L
Sbjct: 78  INTL 81

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 68/180 (37%), Gaps = 44/180 (24%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +  R+FV NL   +TE+++ KLFEKYG   EV +       K KGF  +       A  A
Sbjct: 21  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIA 74
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKN 454
              LD     G+ L +              +  C  +                  + V+N
Sbjct: 75  KVELDNMPLRGKQLRV--------------RFACHSAS-----------------LTVRN 103
Query: 455 LPYRTLPTDLKALFEPFGDLGRVLV------PPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
           LP       L+  F  FG + R +V       P G  G+VEF  K  A+ A +  +   F
Sbjct: 104 LPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSG-KGIVEFSGKPAARKALDRCSEGSF 162

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 47/197 (23%), Positives = 87/197 (44%), Gaps = 38/197 (19%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           + L++ NL  + TE+ +R+ F+K G    V + + K           G+GF++  TR +L
Sbjct: 23  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----------GFGFIRLETR-TL 70
Query: 641 NQALKV-LQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
            +  KV L N  L   Q+ ++ +  +                    + + VRN+P     
Sbjct: 71  AEIAKVELDNMPLRGKQLRVRFACHS--------------------ASLTVRNLPQYVSN 110
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL---YG 756
             +EE F  FG+++  R    +   G   G G VEF  K  A++A+    + + L   + 
Sbjct: 111 ELLEEAFSVFGQVE--RAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFP 168
Query: 757 RRLVLEWAEEADNVEDI 773
           R + +E  ++ D+ E +
Sbjct: 169 RPVTVEPMDQLDDEEGL 185

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A  A  ++
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 399 DGTVFLGRMLHL 410
           + +   GR + +
Sbjct: 126 NESELFGRTIRV 137

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 41/185 (22%), Positives = 86/185 (46%), Gaps = 28/185 (15%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++ NLNFN +   ++           + V   +        ++  +G+V F + E L +
Sbjct: 10  LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIG------MTRKFGYVDFESAEDLEK 63
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK-ILVRNIPFQAKQSE 701
           AL+ L    +  ++I+L+             K K  +  K+  ++ +L +N+P++  Q E
Sbjct: 64  ALE-LTGLKVFGNEIKLE-------------KPKGKDSKKERDARTLLAKNLPYKVTQDE 109
Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
           ++E+F+   E++ V         G  +G  ++EF T+ +A++  +   Q T + GR + L
Sbjct: 110 LKEVFEDAAEIRLVS------KDGKSKGIAYIEFKTEADAEKTFEE-KQGTEIDGRSISL 162
Query: 762 EWAEE 766
            +  E
Sbjct: 163 YYTGE 167

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHA 391
           +++ ++FV  +  T +E DL +LFE+YG + E+ +  D+  +  ++KG   VTF   + A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            +A   L     L  M H I  KP ++E
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSE 88

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S ++ V N+S T T  +L   FE+YGP+ E         D  K +A V     E A +A 
Sbjct: 10  STKLHVGNISPTCTNQELRAKFEEYGPVIEC--------DIVKDYAFVHMERAEDAVEAI 61
Query: 396 QHLDGTVFLGRMLHL 410
           + LD T F G+ +H+
Sbjct: 62  RGLDNTEFQGKRMHV 76

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/169 (23%), Positives = 74/169 (43%), Gaps = 20/169 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           +T L +  L  + T+  +   F+  GPI +  + R  D K+     S GY FV F +   
Sbjct: 14  NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXR--DYKTG---YSFGYAFVDFTSEXD 68
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
             +A+KVL   ++   ++++  +    ES   T               + V N+P     
Sbjct: 69  SQRAIKVLNGITVRNKRLKVSYARPGGESIKDT--------------NLYVTNLPRTITD 114
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
            +++ +F  +G +    + +  + +G  RG  FV +  + EA+ A+ AL
Sbjct: 115 DQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAFVRYNKREEAQEAISAL 162

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV +LS  +T +D+   F  +G +++  +  D  T K+KG+  V+F     A  A  H+
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 399 DGTVFLGRML 408
            G    GR +
Sbjct: 78  GGQWLGGRQI 87

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV NL   V E+ L +LF + GPL +V +  D+E  K K F  V F  PE  + A   L
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 399 DGTVFLGRMLHL 410
           +G    GR +++
Sbjct: 78  NGIRLYGRPINV 89

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FVRNL+ TVTE+ L K F ++G L  V         K K +A + F   + A +A + +
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEEM 65
Query: 399 DGTVFLGRMLHLIPGKP 415
           +G    G  + ++  KP
Sbjct: 66  NGKDLEGENIEIVFAKP 82

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 33/54 (61%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP 388
           E G++FV  L ++ T++ L   F +YG + + ++  DK T++++GF  V F  P
Sbjct: 15  EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A  A  ++
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 399 DGTVFLGRMLHL 410
           + +   GR + +
Sbjct: 65  NESELFGRTIRV 76

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A  A  ++
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 399 DGTVFLGRMLHL 410
           + +   GR + +
Sbjct: 70  NESELFGRTIRV 81

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A  A  ++
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 399 DGTVFLGRMLHL 410
           + +   GR + +
Sbjct: 68  NESELFGRTIRV 79

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK-ETDKTKGFALVTFLMPEHATQAYQ 396
           ++ +  L+  VT+D + ++F  YG +  + +P+++     +KG+A V F  P+ A +A +
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 397 HLDG 400
           H+DG
Sbjct: 66  HMDG 69

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           ++Y+ N+++ +T + +  HF  CG +  VT+   K    P      G+ +++F  +ES+ 
Sbjct: 7   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP-----KGFAYIEFSDKESVR 61
Query: 642 QALKVLQNSSLDEHQIEL--KRSNR 664
            +L  L  S     QI++  KR+NR
Sbjct: 62  TSL-ALDESLFRGRQIKVIPKRTNR 85

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 38/182 (20%), Positives = 76/182 (41%), Gaps = 17/182 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ N+ F  TE+++   F     +  +T A    P +P               + + ++
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----PGNP-----------VLAVQINQDK 53
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
               L+  S+DE    +       + ++  ++R           K+ +  +P      +V
Sbjct: 54  NFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQV 113
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
           +EL  +FG LK   L K    +GL +G+ F E++  N   +A+  L     L  ++L+++
Sbjct: 114 KELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGL-NGMQLGDKKLLVQ 171
Query: 763 WA 764
            A
Sbjct: 172 RA 173

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 29/90 (32%), Positives = 50/90 (55%), Gaps = 9/90 (10%)
Query: 668 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH 727
           S ++ VKR     A Q  S ++V  +P++  + +++E F  FGE+  V++ KK + +G  
Sbjct: 3   SGSSGVKR-----AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHS 56
Query: 728 RGFGFVEFITKNEAKRAMKALCQSTHLYGR 757
           +GFGFV F    E +  +K + Q   + GR
Sbjct: 57  KGFGFVRF---TEYETQVKVMSQRHMIDGR 83

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV ++     ED++ + F  YG +  + L +D+ T  +KG+ALV +   + A  A + L
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 399 DGTVFLGRMLHL 410
           +G   +G+ + +
Sbjct: 89  NGAEIMGQTIQV 100

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 38/182 (20%), Positives = 76/182 (41%), Gaps = 17/182 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ N+ F  TE+++   F     +  +T A    P +P               + + ++
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----PGNP-----------VLAVQINQDK 51
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
               L+  S+DE    +       + ++  ++R           K+ +  +P      +V
Sbjct: 52  NFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQV 111
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
           +EL  +FG LK   L K    +GL +G+ F E++  N   +A+  L     L  ++L+++
Sbjct: 112 KELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGL-NGMQLGDKKLLVQ 169
Query: 763 WA 764
            A
Sbjct: 170 RA 171

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           TLY+ NL+F +TE+ I   F K G I  + +   K         + G+ FV++Y+R    
Sbjct: 20  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK------MKTACGFCFVEYYSRADAE 73
Query: 642 QALKVLQNSSLDEHQI 657
            A++ +  + LD+  I
Sbjct: 74  NAMRYINGTRLDDRII 89

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 39/169 (23%), Positives = 74/169 (43%), Gaps = 20/169 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           +T L +  L  + T+  +   F+  GPI +  + R  D K+     S GY FV F +   
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMR--DYKTG---YSYGYAFVDFTSEMD 57
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
             +A+KVL   ++   ++++  +    ES   T               + V N+P     
Sbjct: 58  SQRAIKVLNGITVRNKRLKVSYARPGGESIKDT--------------NLYVTNLPRTITD 103
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
            +++ +F  +G +    + +  + +G  RG  FV +  + EA+ A+ AL
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAFVRYNKREEAQEAISAL 151

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	787
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-36
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-26
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-36
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-35
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-19
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-34
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-23
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-19
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-05
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-33
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-32
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-30
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-25
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-04
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-32
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-30
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-30
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-25
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-06
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-31
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-21
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-06
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-31
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-17
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-16
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-04
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-30
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-19
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-30
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-21
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-10
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-06
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-06
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-27
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-16
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-04
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-04
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-04
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-27
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-15
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-14
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-27
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-16
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-14
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-04
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-27
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-06
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-04
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-26
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-26
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-26
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-25
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-12
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-24
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-16
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-24
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-19
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-06
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-24
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-11
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-10
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-06
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-04
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-23
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-14
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	7e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-23
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	8e-11
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	8e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-23
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-04
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-23
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-17
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-23
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-04
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-06
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-22
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-11
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-08
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-22
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	8e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-21
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-16
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-21
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-05
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-05
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-21
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-21
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-16
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-14
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-21
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	9e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	8e-05
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	8e-21
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-20
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-04
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-20
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-04
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-20
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-10
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-20
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-05
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-20
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-14
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-11
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-05
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-20
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-09
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-18
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-05
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-20
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-08
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-20
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-20
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-20
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-06
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-16
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	9e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-19
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-19
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-19
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-19
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-18
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-17
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-04
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-19
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-18
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-19
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-13
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-19
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-04
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	9e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	6e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-18
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-18
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-15
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-04
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-12
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-18
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-18
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	7e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-04
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-05
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-04
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-18
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-15
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	9e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	9e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	9e-18
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-17
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-17
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-13
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-08
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-17
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	7e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-17
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	6e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	6e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-04
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-13
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-04
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-17
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-13
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-17
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-14
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-12
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-04
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-14
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-13
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-17
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-17
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-17
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-05
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-17
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-15
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-17
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	8e-17
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-07
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-04
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-11
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-09
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-04
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-16
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-16
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-16
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-16
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-16
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-05
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-16
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-11
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-16
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-05
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-15
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-12
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-10
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	9e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	8e-11
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-15
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-15
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	7e-13
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-04
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-15
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-04
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-04
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-15
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-13
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-12
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-14
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-13
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-12
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-06
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-13
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-14
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-12
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-05
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-14
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-14
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-14
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-14
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-14
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-04
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-10
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-14
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-04
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-07
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-10
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-13
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-09
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-05
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-13
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-10
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-13
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	9e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-11
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	7e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	9e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-13
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-13
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	6e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-12
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-12
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-11
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-10
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-12
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-11
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-11
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-10
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-09
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	6e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-11
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-04
2div_A	99	TRNA selenocysteine associated protein; structural	1e-11
2div_A	99	TRNA selenocysteine associated protein; structural	1e-08
2div_A	99	TRNA selenocysteine associated protein; structural	2e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-11
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-07
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	9e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-10
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	8e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-10
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	7e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-10
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-11
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-11
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-10
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	7e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-09
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-09
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	9e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	8e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-09
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	6e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	7e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	7e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	8e-07
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	4e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	3e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	5e-04
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	7e-04

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  134 bits (338), Expect = 5e-36
 Identities = 38/192 (19%), Positives = 77/192 (40%), Gaps = 9/192 (4%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            LY+ N+ F  TE+++   F     +  +T A      +        + F++F + +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKS------SNVAKQTGSKILVRNIPF 695
           QA+            ++++R +        +           S V   +  K+ +  +P 
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 696 QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY 755
                +V+EL  +FG LK   L K    +GL +G+ F E++  N   +A+  L     L 
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQAIAGL-NGMQLG 182

Query: 756 GRRLVLEWAEEA 767
            ++L+++ A   
Sbjct: 183 DKKLLVQRASVG 194

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  105 bits (264), Expect = 4e-26
 Identities = 40/199 (20%), Positives = 73/199 (36%), Gaps = 17/199 (8%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-----IDKETDKTKGFALVTFLMP 388
           A + R++V N+ + +TE+ +   F     L  +        +  + ++ K FA + F   
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 389 EHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKR 448
           +  TQA    DG +F G+ L +      +    +        S       + VV   + +
Sbjct: 62  DETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENP----SVYVPGVVSTVVPDSAHK 116

Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNS 502
           +  +  LP       +K L   FG L    +     TGL       E++  N    A   
Sbjct: 117 LF-IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175

Query: 503 LAYTKFKEVPLYLEWAPEG 521
           L   +  +  L ++ A  G
Sbjct: 176 LNGMQLGDKKLLVQRASVG 194

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 96.3 bits (240), Expect = 7e-23
 Identities = 33/196 (16%), Positives = 69/196 (35%), Gaps = 28/196 (14%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKP-LPLASVRTTFL------------GMAYIGFKDEKNCN 272
            + V N+P G+ ++ +  +F   + L  +                   A++ F+      
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 273 KALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
           +A+  +   ++G+ L I +             D      M    + +       V     
Sbjct: 66  QAMAFDGIIFQGQSLKIRR-----------PHDYQPLPGMSENPSVY----VPGVVSTVV 110

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
              + ++F+  L   + +D + +L   +GPL    L  D  T  +KG+A   ++      
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170

Query: 393 QAYQHLDGTVFLGRML 408
           QA   L+G     + L
Sbjct: 171 QAIAGLNGMQLGDKKL 186

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 83.9 bits (208), Expect = 1e-18
 Identities = 38/231 (16%), Positives = 74/231 (32%), Gaps = 51/231 (22%)

Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQ 492
           A ++R+  V N+P+      +   F     LG +   P                 +EF  
Sbjct: 2   AMARRL-YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKEN 552
            ++   A  +     F+   L +                               + +   
Sbjct: 61  VDETTQAM-AFDGIIFQGQSLKIRRP---------------------------HDYQPLP 92

Query: 553 TAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 612
              E+    VP V   V       P+    L+I  L     +D ++      GP+ +  +
Sbjct: 93  GMSENPSVYVPGVVSTVV------PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146

Query: 613 ARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
              KD  + G   S GY F ++      +QA+  L    L + ++ ++R++
Sbjct: 147 V--KDSAT-GL--SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 47.3 bits (113), Expect = 4e-06
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           +  +Q+K      G +    L   +  G  + +AF  Y   +    A+   N   +   +
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 88  IKVEKCS 94
           + V++ S
Sbjct: 186 LLVQRAS 192

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score =  129 bits (327), Expect = 9e-36
 Identities = 51/95 (53%), Positives = 63/95 (66%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
              + SGR+FVRNLSYT +E+DL KLF  YGPL+E+  PID  T K KGFA VTF+ PEH
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGK 425
           A +AY  +DG VF GRMLH++P   K+        
Sbjct: 63  AVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 74.6 bits (184), Expect = 2e-16
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            ++ VRN+ + + + ++E+LF A+G L  +  P   + +   +GF FV F+    A +A 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-TKKPKGFAFVTFMFPEHAVKAY 67

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
             +       GR L +  +  
Sbjct: 68  AEV-DGQVFQGRMLHVLPSTI 87

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
                    L+++NL++ S+E+ + + F   GP++ +      D  +  +    G+ FV 
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYP--IDSLT-KK--PKGFAFVT 56

Query: 634 FYTRESLNQALKVLQNSSLD 653
           F   E   +A   +      
Sbjct: 57  FMFPEHAVKAYAEVDGQVFQ 76

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
           + V+NL Y +   DL+ LF  +G L  +  P   +T        V F+    A  A+  +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          Y  ++E L+  F   G ++++     +   K + FAF+ +   + A  A    +      
Sbjct: 18 YTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG 77

Query: 86 SRIKVEK 92
            + V  
Sbjct: 78 RMLHVLP 84

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score =  128 bits (324), Expect = 2e-35
 Identities = 66/98 (67%), Positives = 73/98 (74%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
                   KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRGFGFV
Sbjct: 4   GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVE 771
           +FITK +AK+A  ALC STHLYGRRLVLEWA+    V+
Sbjct: 64  DFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 83.1 bits (206), Expect = 2e-19
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 2/91 (2%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKE-TDKTKGFALVTFLMP 388
                 + +I VRN+ +   + ++ +LF  +G L  V LP     T   +GF  V F+  
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68

Query: 389 EHATQAYQHL-DGTVFLGRMLHLIPGKPKEN 418
           + A +A+  L   T   GR L L     +  
Sbjct: 69  QDAKKAFNALCHSTHLYGRRLVLEWADSEVT 99

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 68.9 bits (169), Expect = 2e-14
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 4/79 (5%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           +  + +  + + ++N+ F + +  IR  F   G + +V + +K      G     G+GFV
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT--GTGA--HRGFGFV 63

Query: 633 QFYTRESLNQALKVLQNSS 651
            F T++   +A   L +S+
Sbjct: 64  DFITKQDAKKAFNALCHST 82

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 50.8 bits (122), Expect = 4e-08
 Identities = 33/99 (33%), Positives = 50/99 (50%), Gaps = 8/99 (8%)

Query: 440 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGL------VEFLQ 492
           QV + ++   ILV+N+P++    +++ LF  FG+L  V +P     TG       V+F+ 
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 493 KNQAKAAFNSLA-YTKFKEVPLYLEWAPEGVFAEAKEKS 530
           K  AK AFN+L   T      L LEWA   V  ++   S
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 48.1 bits (115), Expect = 4e-07
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
          ++  Q +++  F   G +  V+L  K T  G  R F F+ +  +  A+ A +   ++   
Sbjct: 25 FQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL 84

Query: 85 SSR-IKVEK 92
            R + +E 
Sbjct: 85 YGRRLVLEW 93

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  126 bits (320), Expect = 7e-34
 Identities = 37/195 (18%), Positives = 82/195 (42%), Gaps = 26/195 (13%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
            E  E      L+I NLN N +   ++    +      + V   +         +  +G+
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT------NRKFGY 58

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVR 691
           V F + E L +AL+ L    +  ++I+L++             +   +   +    +L +
Sbjct: 59  VDFESAEDLEKALE-LTGLKVFGNEIKLEKP------------KGRDSKKVRAARTLLAK 105

Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS 751
           N+ F   + E++E+F+   E++ V         G  +G  ++EF ++ +A++ ++   Q 
Sbjct: 106 NLSFNITEDELKEVFEDALEIRLVS------QDGKSKGIAYIEFKSEADAEKNLEEK-QG 158

Query: 752 THLYGRRLVLEWAEE 766
             + GR + L +  E
Sbjct: 159 AEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 95.4 bits (238), Expect = 7e-23
 Identities = 33/192 (17%), Positives = 67/192 (34%), Gaps = 30/192 (15%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
             +      +F+ NL+   +  +L     +     ++ + +D  T   + F  V F   E
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAE 65

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRI 449
              +A + L G    G  + L   K ++++                       + R+ R 
Sbjct: 66  DLEKALE-LTGLKVFGNEIKLEKPKGRDSK-----------------------KVRAART 101

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 506
           +L KNL +     +LK +FE   ++   LV   G +     +EF  +  A+         
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEI--RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159

Query: 507 KFKEVPLYLEWA 518
           +     + L + 
Sbjct: 160 EIDGRSVSLYYT 171

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 85.3 bits (212), Expect = 2e-19
 Identities = 36/203 (17%), Positives = 63/203 (31%), Gaps = 45/203 (22%)

Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRT------TFLGMAYIGFKDEKNCNK 273
                 + + NL       +LK     L     +        T     Y+ F+  ++  K
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 274 ALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDI 333
           AL        G ++ + K    +S K   A                              
Sbjct: 70  ALELTGLKVFGNEIKLEKPKGRDSKKVRAAR----------------------------- 100

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
                +  +NLS+ +TED+L ++FE    +      +  +  K+KG A + F     A +
Sbjct: 101 ----TLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEK 151

Query: 394 AYQHLDGTVFLGRMLHLIPGKPK 416
             +   G    GR + L     K
Sbjct: 152 NLEEKQGAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 77.3 bits (191), Expect = 2e-16
 Identities = 36/228 (15%), Positives = 64/228 (28%), Gaps = 69/228 (30%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
           E+ +   + + NL       +LK           + V     TG       V+F      
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDL 67

Query: 497 KAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEE 556
           + A   L   K     + LE                                        
Sbjct: 68  EKALE-LTGLKVFGNEIKLEKP-------------------------------------- 88

Query: 557 DNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 616
                        +  + ++     TL  KNL+FN TED ++  F+    I  V+   K 
Sbjct: 89  -------------KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK- 134

Query: 617 DPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
                    S G  +++F +     + L+  Q + +D   + L  +  
Sbjct: 135 ---------SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 47.6 bits (114), Expect = 2e-06
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             +  +LK    E     D+ +     G  R+F ++ +   +  + AL+      VF +
Sbjct: 23 PNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN 81

Query: 87 RIKVEK 92
           IK+EK
Sbjct: 82 EIKLEK 87

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           + IT+++LK  FE+   +  V    + +GK +  A+I +  E  A+  L+      +   
Sbjct: 109 FNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR 164

Query: 87  RIKV 90
            + +
Sbjct: 165 SVSL 168

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  127 bits (322), Expect = 8e-33
 Identities = 35/192 (18%), Positives = 82/192 (42%), Gaps = 17/192 (8%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMGYGFVQF 634
               + TL++ N   + T+ +IR   +    +A S+ +   +   S        + ++  
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTS------RRFAYIDV 166

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP 694
            ++E     ++ L    ++ + +  K SN          K K ++ A   G +I++RN+ 
Sbjct: 167 TSKEDARYCVEKLNGLKIEGYTLVTKVSNPL-------EKSKRTDSATLEGREIMIRNLS 219

Query: 695 FQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH 753
            +   ++ + E F+ FG ++ + +P        +    F+ F  K+ A+RA++     + 
Sbjct: 220 TELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM--NRSL 277

Query: 754 LYGRRLVLEWAE 765
           L  R + +  A+
Sbjct: 278 LGNREISVSLAD 289

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  126 bits (318), Expect = 2e-32
 Identities = 38/220 (17%), Positives = 81/220 (36%), Gaps = 34/220 (15%)

Query: 547 EEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP 606
               +   +E +        +   E   R  E  TT+ +KNL  +  ++ + ++FK CGP
Sbjct: 9   RPDSKRPLDEGSPAAAGLTSKKANEALTRNRE-LTTVLVKNLPKSYNQNKVYKYFKHCGP 67

Query: 607 IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNL 666
           I  V VA            +  +  ++F   +    A+    +  + +++I         
Sbjct: 68  IIHVDVADSLKK-------NFRFARIEFARYDGALAAITKT-HKVVGQNEII-------- 111

Query: 667 ESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSG 725
                        V+  T   + + N P    Q  + +L +    +   +RLP     + 
Sbjct: 112 -------------VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT- 157

Query: 726 LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
             R F +++  +K +A+  ++ L     + G  LV + + 
Sbjct: 158 -SRRFAYIDVTSKEDARYCVEKL-NGLKIEGYTLVTKVSN 195

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  120 bits (302), Expect = 3e-30
 Identities = 49/369 (13%), Positives = 109/369 (29%), Gaps = 93/369 (25%)

Query: 303 AADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGP 362
           A  D+     E   A    + + + +      E   + V+NL  +  ++ + K F+  GP
Sbjct: 8   ARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGP 67

Query: 363 LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNV 422
           +  V +       K   FA + F   + A  A       V                    
Sbjct: 68  IIHVDVA--DSLKKNFRFARIEFARYDGALAAITKTHKVVG---------QNEI------ 110

Query: 423 DGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY 482
                             +V   ++  + + N P      +++ L +    +   +  P 
Sbjct: 111 ------------------IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS 152

Query: 483 GITGL------VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKE 536
                      ++   K  A+     L   K +   L  + +           +  ++ +
Sbjct: 153 LRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS-----------NPLEKSK 201

Query: 537 KNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNST-ED 595
           + +    EG                                     + I+NL+     E+
Sbjct: 202 RTDSATLEG-----------------------------------REIMIRNLSTELLDEN 226

Query: 596 SIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH 655
            +R  F+  G I  + +   +   S     +    F+ F  ++S  +AL+ +  S L   
Sbjct: 227 LLRESFEGFGSIEKINIPAGQKEHSF----NNCCAFMVFENKDSAERALQ-MNRSLLGNR 281

Query: 656 QIELKRSNR 664
           +I +  +++
Sbjct: 282 EISVSLADK 290

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  105 bits (263), Expect = 5e-25
 Identities = 51/318 (16%), Positives = 96/318 (30%), Gaps = 75/318 (23%)

Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-----LGMAYIGFKDE 268
           ++A    R+  T++VKNLP    +  +  YFK   P+  V            A I F   
Sbjct: 32  NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARY 91

Query: 269 KNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQ 328
                A+ K        ++ +   ++                                  
Sbjct: 92  DGALAAITKTHKVVGQNEIIVSHLTECT-------------------------------- 119

Query: 329 FAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP 388
                     +++ N   + T+ ++  L +    +A  I       + ++ FA +     
Sbjct: 120 ----------LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSK 169

Query: 389 EHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKR 448
           E A    + L+G    G  L      P E     D             A  +  E     
Sbjct: 170 EDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDS------------ATLEGRE----- 212

Query: 449 IILVKNLPYRTLP-TDLKALFEPFGDLGRVLVPPYGIT-------GLVEFLQKNQAKAAF 500
            I+++NL    L    L+  FE FG + ++ +P              + F  K+ A+ A 
Sbjct: 213 -IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271

Query: 501 NSLAYTKFKEVPLYLEWA 518
             +  +      + +  A
Sbjct: 272 Q-MNRSLLGNREISVSLA 288

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 50.0 bits (120), Expect = 1e-06
 Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 27  YKITQEQLKAKFEEKGTVT-DVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
              TQ  ++   ++   V   ++L        RRFA+I    ++ A+  ++  N   +  
Sbjct: 127 PSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG 186

Query: 86  SRIKVEK 92
             +  + 
Sbjct: 187 YTLVTKV 193

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 42.7 bits (101), Expect = 3e-04
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
               Q ++   F+  G +  V +   +  K  RFA I + R D A AA+   +   V  +
Sbjct: 51  KSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTHK-VVGQN 108

Query: 87  RIKVEKCSN 95
            I V   + 
Sbjct: 109 EIIVSHLTE 117

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  124 bits (314), Expect = 8e-32
 Identities = 56/348 (16%), Positives = 89/348 (25%), Gaps = 101/348 (29%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
                  +I +R L   VT  ++  L   Y              DK KG A VT L  E 
Sbjct: 17  RQFRNRRKILIRGLPGDVTNQEVHDLLSDYELK-------YCFVDKYKGTAFVTLLNGEQ 69

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRII 450
           A  A      +    R L                                V    +  ++
Sbjct: 70  AEAAINAFHQSRLREREL-------------------------------SVQLQPTDALL 98

Query: 451 LVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLA 504
            V NLP        + L  PFG L R  +     TG        E+++K+ A  A + L 
Sbjct: 99  CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL 158

Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE 564
                   LY+ W   G    A   S+                                 
Sbjct: 159 GKPLGPRTLYVHWTDAGQLTPALLHSR--------------------------------- 185

Query: 565 VEENVEEDEEREPEPDTTLYIKNLNFNSTE-DSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
                             L +  L     + D++ R            +A  +D +    
Sbjct: 186 -----------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQ---- 224

Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEAT 671
               G+  +++ T E   +A +     SL    + +          + 
Sbjct: 225 --LKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSM 270

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  120 bits (303), Expect = 2e-30
 Identities = 42/212 (19%), Positives = 69/212 (32%), Gaps = 34/212 (16%)

Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
           E  ER+      + I+ L  + T   +         +    V + K           G  
Sbjct: 13  EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK-----------GTA 60

Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILV 690
           FV     E    A+     S L E ++ ++                       T + + V
Sbjct: 61  FVTLLNGEQAEAAINAFHQSRLRERELSVQLQ--------------------PTDALLCV 100

Query: 691 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ 750
            N+P    Q + EEL + FG L+   L      +G  +G+GF E++ K+ A RA   L  
Sbjct: 101 ANLPPSLTQQQFEELVRPFGSLERCFLVYSER-TGQSKGYGFAEYMKKDSAARAKSDL-L 158

Query: 751 STHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
              L  R L + W +       +         
Sbjct: 159 GKPLGPRTLYVHWTDAGQLTPALLHSRCLCVD 190

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  118 bits (298), Expect = 9e-30
 Identities = 34/196 (17%), Positives = 65/196 (33%), Gaps = 20/196 (10%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +    D  L + NL  + T+       +  G +    +      ++ GQ  S GYGF ++
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY--SERT-GQ--SKGYGFAEY 144

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP 694
             ++S  +A   L    L    + +  ++    + A      S          + V  +P
Sbjct: 145 MKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPA---LLHSRC--------LCVDRLP 193

Query: 695 FQAKQSE-VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH 753
                 + +     A     F +L       G  +GF  +E+ T   A+ A +       
Sbjct: 194 PGFNDVDALCRALSAVHSPTFCQLACGQ--DGQLKGFAVLEYETAEMAEEAQQQA-DGLS 250

Query: 754 LYGRRLVLEWAEEADN 769
           L G  L + +      
Sbjct: 251 LGGSHLRVSFCAPGPP 266

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  105 bits (263), Expect = 4e-25
 Identities = 41/304 (13%), Positives = 83/304 (27%), Gaps = 77/304 (25%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTF-LGMAYIGFKDEKNCNKALNK-NKSFWK 283
            I+++ LP  V  +++        L         G A++   + +    A+N  ++S  +
Sbjct: 24  KILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLR 83

Query: 284 GKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRN 343
            ++L                                      SVQ          + V N
Sbjct: 84  EREL--------------------------------------SVQLQP---TDALLCVAN 102

Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
           L  ++T+    +L   +G L    L   + T ++KG+    ++  + A +A   L G   
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162

Query: 404 LGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTD 463
             R L++      +                              R + V  LP      D
Sbjct: 163 GPRTLYVHWTDAGQLTP----------------------ALLHSRCLCVDRLPPGFNDVD 200

Query: 464 -LKALFEPFGDLGRVLVPP--------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY 514
            L              +          + +   +E+     A+ A             L 
Sbjct: 201 ALCRALSAVHSPTFCQLACGQDGQLKGFAV---LEYETAEMAEEAQQQADGLSLGGSHLR 257

Query: 515 LEWA 518
           + + 
Sbjct: 258 VSFC 261

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 75.8 bits (187), Expect = 4e-15
 Identities = 28/207 (13%), Positives = 58/207 (28%), Gaps = 43/207 (20%)

Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-------LGMAYIGFKDEKNCNK 273
                + V NLP  + ++  +   +P   L      +        G  +  +  + +  +
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 274 ALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
           A +         + L ++               D    +   + ++              
Sbjct: 153 AKSDLLGKPLGPRTLYVHWT-------------DAGQLTPALLHSR-------------- 185

Query: 333 IAESGRIFVRNLSYTVTEDD-LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
                 + V  L     + D L +            L    +  + KGFA++ +   E A
Sbjct: 186 -----CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMA 239

Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            +A Q  DG    G  L +    P   
Sbjct: 240 EEAQQQADGLSLGGSHLRVSFCAPGPP 266

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 48.4 bits (116), Expect = 3e-06
 Identities = 20/113 (17%), Positives = 41/113 (36%), Gaps = 18/113 (15%)

Query: 409 HLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALF 468
           H++  +               +   +        + R++R IL++ LP      ++  L 
Sbjct: 1   HMLDPEEIRKR----------LEHTE-------RQFRNRRKILIRGLPGDVTNQEVHDLL 43

Query: 469 EPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG 521
             +      +    G T  V  L   QA+AA N+   ++ +E  L ++  P  
Sbjct: 44  SDYELKYCFVDKYKG-TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 48.4 bits (116), Expect = 4e-06
 Identities = 12/60 (20%), Positives = 24/60 (40%)

Query: 31  QEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV 90
            + L        + T  QL    +G+ + FA + Y   + A+ A    +   +  S ++V
Sbjct: 199 VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 48.1 bits (115), Expect = 5e-06
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 1/66 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
             +TQ+Q +      G++    L Y+   G+ + + F  Y ++D A  A        +  
Sbjct: 105 PSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164

Query: 86  SRIKVE 91
             + V 
Sbjct: 165 RTLYVH 170

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  121 bits (305), Expect = 2e-31
 Identities = 39/192 (20%), Positives = 90/192 (46%), Gaps = 10/192 (5%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                 + +Y+ ++ +   ED+IR+ F   GPI S+ ++   D  +       G+ FV++
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW--DSVTMK---HKGFAFVEY 77

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP 694
              E+   AL+ + +  L    I++ R +   +++    +        +  ++I V ++ 
Sbjct: 78  EVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA---RAFNRIYVASVH 134

Query: 695 FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL 754
                 +++ +F+AFG++K   L +    +G H+G+GF+E+     ++ A+ ++     L
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDP-TTGKHKGYGFIEYEKAQSSQDAVSSM-NLFDL 192

Query: 755 YGRRLVLEWAEE 766
            G+ L +  A  
Sbjct: 193 GGQYLRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 97.4 bits (243), Expect = 4e-23
 Identities = 43/215 (20%), Positives = 86/215 (40%), Gaps = 20/215 (9%)

Query: 310 ASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP 369
           + M ++       +  + Q    +A   R++V ++ Y + ED + + F  +GP+  + + 
Sbjct: 2   SHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMS 61

Query: 370 IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCC 429
            D  T K KGFA V + +PE A  A + ++  +  GR + +                   
Sbjct: 62  WDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI------------- 108

Query: 430 ISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL-- 487
             + +        EAR+   I V ++       D+K++FE FG +    +     TG   
Sbjct: 109 -GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHK 167

Query: 488 ----VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
               +E+ +   ++ A +S+         L +  A
Sbjct: 168 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 90.8 bits (226), Expect = 6e-21
 Identities = 36/221 (16%), Positives = 76/221 (34%), Gaps = 37/221 (16%)

Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR-------TT 256
                +        +  R Y    V ++   + +  ++  F P  P+ S+          
Sbjct: 13  MGRGSAAQRQGALAIMSRVY----VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK 68

Query: 257 FLGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENI 315
             G A++ ++  +    AL + N     G+ + + + S    A                 
Sbjct: 69  HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA----------------- 111

Query: 316 KAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD 375
                  Q    Q AE+     RI+V ++   +++DD+  +FE +G +    L  D  T 
Sbjct: 112 -------QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG 164

Query: 376 KTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK 416
           K KG+  + +   + +  A   ++     G+ L +      
Sbjct: 165 KHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 81.6 bits (202), Expect = 1e-17
 Identities = 34/219 (15%), Positives = 74/219 (33%), Gaps = 53/219 (24%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAY 505
           V ++ Y      ++  F PFG +  + +    +T        VE+     A+ A   +  
Sbjct: 33  VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92

Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
                  + +              S   + +   ++  E                     
Sbjct: 93  VMLGGRNIKVGRP-----------SNIGQAQPIIDQLAE--------------------- 120

Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
                     E      +Y+ +++ + ++D I+  F+  G I S T+AR  DP + G+  
Sbjct: 121 ----------EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR--DPTT-GK-- 165

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
             GYGF+++   +S   A+  +    L    + + ++  
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 47.3 bits (113), Expect = 5e-06
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           ++ + +K+ FE  G +    L      GK + + FI Y +   +Q A+   N   +    
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 196

Query: 88  IKV 90
           ++V
Sbjct: 197 LRV 199

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 21/93 (22%), Positives = 46/93 (49%), Gaps = 3/93 (3%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           Y++ ++ ++  F   G +  + + + +   K + FAF+ Y   + AQ AL+  N+  +  
Sbjct: 38  YELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 97

Query: 86  SRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKL 118
             IKV + SN+G         + A ++ A+ ++
Sbjct: 98  RNIKVGRPSNIGQ--AQPIIDQLAEEARAFNRI 128

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score =  117 bits (294), Expect = 2e-31
 Identities = 50/109 (45%), Positives = 66/109 (60%)

Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKA 498
           +     RSK +IL KNLP  TL  +++  F  FG LGRVL+P  GIT +VEFL+  +A+ 
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARK 61

Query: 499 AFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEE 547
           AF  LAY+KF  VPLYLEWAP GVF  A +K   + ++  E+       
Sbjct: 62  AFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSS 110

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 76.8 bits (189), Expect = 4e-17
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I  +NL       ++ + F ++G L  V+LP      +    A+V FL P  A +A++HL
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHL 66

Query: 399 DGTVFLGRMLHL 410
             + F    L+L
Sbjct: 67  AYSKFHHVPLYL 78

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 72.9 bits (179), Expect = 9e-16
 Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 8/103 (7%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
           SS  + ++ + IL +N+P     +E++E F  FG L  V LP+             VEF+
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-------GITAIVEFL 54

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
              EA++A + L   +  +   L LEWA         +K+ ++
Sbjct: 55  EPLEARKAFRHL-AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQ 96

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 58.3 bits (141), Expect = 1e-10
 Identities = 16/104 (15%), Positives = 30/104 (28%), Gaps = 11/104 (10%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
            T +  KNL   +    I+  F + G +  V +                   V+F     
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-----------ITAIVEFLEPLE 58

Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQ 683
             +A + L  S      + L+ +   +   A   K        +
Sbjct: 59  ARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAE 102

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 41.7 bits (98), Expect = 9e-05
 Identities = 8/66 (12%), Positives = 22/66 (33%), Gaps = 5/66 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
                +++  F   G++  V L      +    A + +    +A+ A  +   +     
Sbjct: 20 AGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFHHV 74

Query: 87 RIKVEK 92
           + +E 
Sbjct: 75 PLYLEW 80

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.0 bits (91), Expect = 6e-04
 Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 2/62 (3%)

Query: 218 PVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT-FLGMAYIGFKDEKNCNKAL 275
               R    I+ KNLPAG    +++  F     L  V        A + F +     KA 
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAF 63

Query: 276 NK 277
             
Sbjct: 64  RH 65

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  117 bits (296), Expect = 1e-30
 Identities = 38/183 (20%), Positives = 76/183 (41%), Gaps = 17/183 (9%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            LY+ N+ F  TE+++   F     +  +T A      +        + F++F + +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
           QA+        D    +     ++L+     ++R           K+ +  +P      +
Sbjct: 66  QAMA------FDGIIFQ----GQSLK-----IRRPHDYQPLPGAHKLFIGGLPNYLNDDQ 110

Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
           V+EL  +FG LK   L K    +GL +G+ F E++  N   +A+  L     L  ++L++
Sbjct: 111 VKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQAIAGL-NGMQLGDKKLLV 168

Query: 762 EWA 764
           + A
Sbjct: 169 QRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 85.0 bits (211), Expect = 2e-19
 Identities = 37/197 (18%), Positives = 68/197 (34%), Gaps = 37/197 (18%)

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-----IDKETDKTKGFALVTFLM 387
           +  + R++V N+ + +TE+ +   F     L  +        +  + ++ K FA + F  
Sbjct: 1   LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 388 PEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSK 447
            +  TQA    DG +F G+   L   +P  +   + G                       
Sbjct: 61  VDETTQAMA-FDGIIFQGQ--SLKIRRPH-DYQPLPGAHK-------------------- 96

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFN 501
             + +  LP       +K L   FG L    +     TGL       E++  N    A  
Sbjct: 97  --LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154

Query: 502 SLAYTKFKEVPLYLEWA 518
            L   +  +  L ++ A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 80.7 bits (200), Expect = 7e-18
 Identities = 31/196 (15%), Positives = 67/196 (34%), Gaps = 48/196 (24%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKP-LPLASVRTTF------------LGMAYIGFKDEKNCN 272
            + V N+P G+ ++ +  +F   + L  +                   A++ F+      
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 273 KALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
           +A+  +   ++G+ L I +   D                                   + 
Sbjct: 66  QAMAFDGIIFQGQSLKI-RRPHDY----------------------------------QP 90

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           +  + ++F+  L   + +D + +L   +GPL    L  D  T  +KG+A   ++      
Sbjct: 91  LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 150

Query: 393 QAYQHLDGTVFLGRML 408
           QA   L+G     + L
Sbjct: 151 QAIAGLNGMQLGDKKL 166

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 64.2 bits (157), Expect = 4e-12
 Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +       L+I  L     +D ++      GP+ +  + +  D  + G   S GY F ++
Sbjct: 89  QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK--DSAT-GL--SKGYAFCEY 143

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSN 663
                 +QA+  L    L + ++ ++R++
Sbjct: 144 VDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 42.2 bits (100), Expect = 2e-04
 Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 1/65 (1%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           +  +Q+K      G +    L   +  G  + +AF  Y   +    A+   N   +   +
Sbjct: 106 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 165

Query: 88  IKVEK 92
           + V++
Sbjct: 166 LLVQR 170

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  116 bits (294), Expect = 2e-30
 Identities = 41/187 (21%), Positives = 81/187 (43%), Gaps = 17/187 (9%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
             +++  +    +E  +R  F++ G +  + V R  D        S G  FV FYTR++ 
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR--DRSQ-NPPQSKGCCFVTFYTRKAA 60

Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
            +A   L N  +        +               S         K+ +  I  +  ++
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMK----------PADSEKNNAVEDRKLFIGMISKKCTEN 110

Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG--RR 758
           ++  +F +FG+++  R+ +     GL RG  FV F T+  A+ A+KA+ Q+  + G    
Sbjct: 111 DIRVMFSSFGQIEECRILRGP--DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 168

Query: 759 LVLEWAE 765
           +V+++A+
Sbjct: 169 MVVKFAD 175

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 91.9 bits (229), Expect = 1e-21
 Identities = 48/194 (24%), Positives = 87/194 (44%), Gaps = 31/194 (15%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET--DKTKGFALVTFLMPEHAT 392
           ++ ++FV  +  T +E DL +LFE+YG + E+ +  D+     ++KG   VTF   + A 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILV 452
           +A   L     L  M H I  KP ++E N   +      +RKL  F             +
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVE------DRKL--F-------------I 100

Query: 453 KNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYTK 507
             +  +    D++ +F  FG +   R+L  P G++     V F  +  A+ A  ++   +
Sbjct: 101 GMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 160

Query: 508 FKEV---PLYLEWA 518
             E    P+ +++A
Sbjct: 161 TMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 68.4 bits (168), Expect = 2e-13
 Identities = 29/192 (15%), Positives = 57/192 (29%), Gaps = 47/192 (24%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR---------TTFLGMAYIGFKDEKNCNKA- 274
            + V  +P    +KDL+  F+    +  +              G  ++ F   K   +A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 275 --LNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
             L+  K           K +                                      +
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEK---------------------------------NN 91

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
             E  ++F+  +S   TE+D+  +F  +G + E  +        ++G A VTF     A 
Sbjct: 92  AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQ 150

Query: 393 QAYQHLDGTVFL 404
            A + +     +
Sbjct: 151 TAIKAMHQAQTM 162

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 65.3 bits (160), Expect = 2e-12
 Identities = 41/211 (19%), Positives = 61/211 (28%), Gaps = 63/211 (29%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--------VEFLQKNQAKAAFNSL 503
           V  +P      DL+ LFE +G +  + V                V F  +  A  A N+L
Sbjct: 8   VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67

Query: 504 AYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVP 563
              K                          + +  + E     E++K             
Sbjct: 68  HNMKVLP-----------------GMHHPIQMKPADSEKNNAVEDRK------------- 97

Query: 564 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
                              L+I  ++   TE+ IR  F   G I    + R  D    G 
Sbjct: 98  -------------------LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD----GL 134

Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDE 654
             S G  FV F TR     A+K +  +   E
Sbjct: 135 --SRGCAFVTFTTRAMAQTAIKAMHQAQTME 163

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 58.8 bits (143), Expect = 3e-10
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 1/97 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAM 745
           K+ V  +P    + ++ ELF+ +G +  + + + +       +G  FV F T+  A  A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 746 KALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
            AL     L G    ++         +  +    + G
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIG 101

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 48.4 bits (116), Expect = 1e-06
 Identities = 11/57 (19%), Positives = 23/57 (40%)

Query: 28  KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
           K T+  ++  F   G + + ++    +G  R  AF+ +     AQ A+   +     
Sbjct: 106 KCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTM 162

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 48.0 bits (115), Expect = 1e-06
 Identities = 10/65 (15%), Positives = 26/65 (40%), Gaps = 3/65 (4%)

Query: 29 ITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           +++ L+  FE+ G V ++ +   +     + +   F+ ++    A  A +  +N  V  
Sbjct: 15 WSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLP 74

Query: 86 SRIKV 90
               
Sbjct: 75 GMHHP 79

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  112 bits (281), Expect = 1e-27
 Identities = 39/213 (18%), Positives = 77/213 (36%), Gaps = 35/213 (16%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
            +  E+       L++ NL  + TE+  +R F++ G  + V + R +           G+
Sbjct: 12  LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-----------GF 60

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKIL 689
           GF++  +R     A   L  + L    + ++ +                      G+ + 
Sbjct: 61  GFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH--------------------GAALT 100

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRAMKAL 748
           V+N+        +E+ F  FG ++   +   +V   G   G GFVEF  K  A++A++  
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVV---VVDDRGRATGKGFVEFAAKPPARKALERC 157

Query: 749 CQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
                L          E  +  +D      +  
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLM 190

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 77.0 bits (190), Expect = 9e-16
 Identities = 45/178 (25%), Positives = 64/178 (35%), Gaps = 42/178 (23%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           +   +  R+FV NL   +TE+D  +LFE+YG  +EV +  D+      GF  +       
Sbjct: 17  KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTL 70

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRII 450
           A  A   LDGT+   R L                               ++  A     +
Sbjct: 71  AEIAKAELDGTILKSRPL-------------------------------RIRFATHGAAL 99

Query: 451 LVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSL 503
            VKNL        L+  F  FG +    V+V   G     G VEF  K  A+ A    
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERC 157

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 65.9 bits (161), Expect = 5e-12
 Identities = 38/208 (18%), Positives = 71/208 (34%), Gaps = 46/208 (22%)

Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-LGMAYIGFKDEKNCNKALNK- 277
             Q   + V NLP  + ++D K  F+     + V      G  +I  +       A  + 
Sbjct: 19  YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 78

Query: 278 NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESG 337
           + +  K + L                                       ++FA       
Sbjct: 79  DGTILKSRPLR--------------------------------------IRFAT---HGA 97

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            + V+NLS  V+ + L + F ++GP+ + ++ +D +  +  G   V F     A +A + 
Sbjct: 98  ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALER 156

Query: 398 L-DGTVFLGRMLHLIPGKPKENEGNVDG 424
             DG   L      +  +P E   + DG
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDEDG 184

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 5/66 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            IT+E  K  FE  G  ++V +      + R F FI       A+ A    + T + S 
Sbjct: 32 TDITEEDFKRLFERYGEPSEVFI-----NRDRGFGFIRLESRTLAEIAKAELDGTILKSR 86

Query: 87 RIKVEK 92
           +++  
Sbjct: 87 PLRIRF 92

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 6/73 (8%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKF 508
           V NLP      D K LFE +G+   V +     +   G +    +  A+ A   L  T  
Sbjct: 27  VGNLPTDITEEDFKRLFERYGEPSEVFINRDRGF---GFIRLESRTLAEIAKAELDGTIL 83

Query: 509 KEVPLYLEWAPEG 521
           K  PL + +A  G
Sbjct: 84  KSRPLRIRFATHG 96

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 10/59 (16%), Positives = 23/59 (38%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           ++ E L+  F + G V    +     G+     F+ +  +  A+ AL+   +     + 
Sbjct: 108 VSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTT 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score =  107 bits (269), Expect = 4e-27
 Identities = 44/185 (23%), Positives = 86/185 (46%), Gaps = 20/185 (10%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            LY+ NL+   TED ++++F+  GPIA++ +   K+ K      ++ Y FV+++     N
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK------NVNYAFVEYHQSHDAN 55

Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
            AL+ L    ++ + +++  + +            S   +      + V ++        
Sbjct: 56  IALQTLNGKQIENNIVKINWAFQ------------SQQSSSDDTFNLFVGDLNVNVDDET 103

Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
           +   FK F       +   M  +G  RG+GFV F ++++A+ AM ++ Q   L GR L +
Sbjct: 104 LRNAFKDFPSYLSGHVMWDMQ-TGSSRGYGFVSFTSQDDAQNAMDSM-QGQDLNGRPLRI 161

Query: 762 EWAEE 766
            WA +
Sbjct: 162 NWAAK 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 75.6 bits (187), Expect = 4e-16
 Identities = 31/189 (16%), Positives = 64/189 (33%), Gaps = 41/189 (21%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNK- 277
            + V NL   + +  LK YF+   P+A+++         +  A++ +    + N AL   
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 278 NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESG 337
           N    +   + I    +   +                                     + 
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDD---------------------------------TF 88

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +FV +L+  V ++ L   F+ +       +  D +T  ++G+  V+F   + A  A   
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 398 LDGTVFLGR 406
           + G    GR
Sbjct: 149 MQGQDLNGR 157

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 74.5 bits (184), Expect = 1e-15
 Identities = 38/225 (16%), Positives = 74/225 (32%), Gaps = 67/225 (29%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--------PYGITGLVEFLQKNQAKAA 499
           R++ V NL        LK  F+  G +  + +          Y     VE+ Q + A  A
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYA---FVEYHQSHDANIA 57

Query: 500 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ 559
             +L   + +   + + WA                                         
Sbjct: 58  LQTLNGKQIENNIVKINWA----------------------------------------- 76

Query: 560 QGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
                      + ++   +    L++ +LN N  ++++R  FK      S  V    D +
Sbjct: 77  ----------FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW--DMQ 124

Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
           + G   S GYGFV F +++    A+  +Q   L+   + +  + +
Sbjct: 125 T-GS--SRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 71.0 bits (175), Expect = 1e-14
 Identities = 41/191 (21%), Positives = 68/191 (35%), Gaps = 40/191 (20%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V NL   +TED L + F+  GP+A + + IDK  +K   +A V +     A  A Q L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 399 DGTVFLGRMLHL-----IPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK 453
           +G      ++ +           ++  N+               F             V 
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNL---------------F-------------VG 93

Query: 454 NLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAYTK 507
           +L        L+  F+ F       V     TG       V F  ++ A+ A +S+    
Sbjct: 94  DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 153

Query: 508 FKEVPLYLEWA 518
               PL + WA
Sbjct: 154 LNGRPLRINWA 164

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 47.5 bits (114), Expect = 2e-06
 Identities = 16/68 (23%), Positives = 32/68 (47%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            IT++ LK  F+  G + ++++      K   +AF+ YH+   A  AL   N   + ++
Sbjct: 10 KAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENN 69

Query: 87 RIKVEKCS 94
           +K+    
Sbjct: 70 IVKINWAF 77

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  107 bits (270), Expect = 6e-27
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 19/189 (10%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
           +  +EPE    L+I  L+F +T++S+R HF++ G +    V   +DP +  +  S G+GF
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV--MRDPNT-KR--SRGFGF 59

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVR 691
           V + T E ++ A+   +   +D   +E KR        A + +      A  T  KI V 
Sbjct: 60  VTYATVEEVDAAMNA-RPHKVDGRVVEPKR--------AVSREDSQRPGAHLTVKKIFVG 110

Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS 751
            I    ++  + + F+ +G+++ + +     GSG  RGF FV F   +      K + Q 
Sbjct: 111 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDSVD---KIVIQK 166

Query: 752 TH-LYGRRL 759
            H + G   
Sbjct: 167 YHTVNGHNC 175

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 76.6 bits (189), Expect = 4e-16
 Identities = 30/151 (19%), Positives = 59/151 (39%), Gaps = 22/151 (14%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           ++  +  ++F+  LS+  T++ L   FE++G L + ++  D  T +++GF  VT+   E 
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGK-VHCCISERKLDAFNQVVEARSKRI 449
              A                           VDG+ V    +  + D+         K+ 
Sbjct: 68  VDAAM--------------------NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK- 106

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 480
           I V  +   T    L+  FE +G +  + + 
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 72.3 bits (178), Expect = 1e-14
 Identities = 37/212 (17%), Positives = 68/212 (32%), Gaps = 38/212 (17%)

Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASV-----RTTFL--GMAYIGFK 266
           S++P    Q   + +  L      + L+++F+    L          T    G  ++ + 
Sbjct: 4   SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63

Query: 267 DEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDS 326
             +  + A+N       G+ +                              K   S+EDS
Sbjct: 64  TVEEVDAAMNARPHKVDGRVVEP----------------------------KRAVSREDS 95

Query: 327 VQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL 386
            Q         +IFV  +     E  L   FE+YG +  + +  D+ + K +GFA VTF 
Sbjct: 96  -QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

Query: 387 MPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
             +   +           G    +     K+ 
Sbjct: 155 DHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE 185

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 51.5 bits (124), Expect = 1e-07
 Identities = 12/93 (12%), Positives = 40/93 (43%), Gaps = 6/93 (6%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
           +            +++  +  ++ E  +R +F++ G I  + +   +           G+
Sbjct: 94  DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKR-----GF 148

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRS 662
            FV F   +S+++ +   +  +++ H  E++++
Sbjct: 149 AFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA 180

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 50.4 bits (121), Expect = 3e-07
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
           K +S    +Q   K+ +  + F+     +   F+ +G L    + +    +   RGFGFV
Sbjct: 3   KSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSRGFGFV 60

Query: 734 EFITKNEAKRAMKA 747
            + T  E   AM A
Sbjct: 61  TYATVEEVDAAMNA 74

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 40.7 bits (96), Expect = 6e-04
 Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
             +  L+  FE+ G +  +++      GK R FAF+ +   D     +
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  106 bits (268), Expect = 6e-27
 Identities = 36/169 (21%), Positives = 71/169 (42%), Gaps = 20/169 (11%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           +T L +  L  + T+  +   F+  GPI +  + R           S GY FV F +   
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGY-----SYGYAFVDFTSEMD 57

Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
             +A+KVL   ++   ++++  +    ES                 + + V N+P     
Sbjct: 58  SQRAIKVLNGITVRNKRLKVSYARPGGESI--------------KDTNLYVTNLPRTITD 103

Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
            +++ +F  +G +    + +  + +G  RG  FV +  + EA+ A+ AL
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAFVRYNKREEAQEAISAL 151

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 89.6 bits (223), Expect = 6e-21
 Identities = 37/193 (19%), Positives = 69/193 (35%), Gaps = 33/193 (17%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           A +  + V  L   +T+ +L  LF   GP+    +  D +T  + G+A V F     + +
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK 453
           A + L+G     + L +   +P                   +   N          + V 
Sbjct: 61  AIKVLNGITVRNKRLKVSYARP---------------GGESIKDTN----------LYVT 95

Query: 454 NLPYRTLPTDLKALFEPFGDL--GRVLV-PPYGIT---GLVEFLQKNQAKAAFNSL--AY 505
           NLP       L  +F  +G +    +L     G       V + ++ +A+ A ++L    
Sbjct: 96  NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155

Query: 506 TKFKEVPLYLEWA 518
            +    PL +  A
Sbjct: 156 PEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 74.1 bits (183), Expect = 1e-15
 Identities = 41/187 (21%), Positives = 74/187 (39%), Gaps = 44/187 (23%)

Query: 229 VKNLPAGVKKKDLKAYFKPL-PLASV-----RTTF--LGMAYIGFKDEKNCNKALNK-NK 279
           V  LP  +  ++L A F+ + P+ +        T    G A++ F  E +  +A+   N 
Sbjct: 8   VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67

Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRI 339
              + K+L +      + A+  G +  + N                             +
Sbjct: 68  ITVRNKRLKV------SYARPGGESIKDTN-----------------------------L 92

Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
           +V NL  T+T+D L  +F KYG + +  +  DK T + +G A V +   E A +A   L+
Sbjct: 93  YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

Query: 400 GTVFLGR 406
             +  G 
Sbjct: 153 NVIPEGG 159

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 73.4 bits (181), Expect = 3e-15
 Identities = 43/214 (20%), Positives = 66/214 (30%), Gaps = 64/214 (29%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 499
           S   ++V  LP      +L ALF   G +    +     TG       V+F  +  ++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 500 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ 559
              L     +   L + +A             G E  K                      
Sbjct: 62  IKVLNGITVRNKRLKVSYA-----------RPGGESIK---------------------- 88

Query: 560 QGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
                               DT LY+ NL    T+D +   F K G I    + R  D  
Sbjct: 89  --------------------DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR--DKL 126

Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
           + G+    G  FV++  RE   +A+  L N   +
Sbjct: 127 T-GR--PRGVAFVRYNKREEAQEAISALNNVIPE 157

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 46.0 bits (110), Expect = 6e-06
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
            +T  +L A F   G +   ++     T  G    +AF+ +  E  +Q A+   N   V
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKT--GYSYGYAFVDFTSEMDSQRAIKVLNGITV 70

Query: 84 FSSRIKV 90
           + R+KV
Sbjct: 71 RNKRLKV 77

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 41.4 bits (98), Expect = 3e-04
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYV 83
           IT +QL   F + G++    +      G+ R  AF+ Y++ ++AQ A+   NN   
Sbjct: 101 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP 156

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  104 bits (262), Expect = 4e-26
 Identities = 42/168 (25%), Positives = 69/168 (41%), Gaps = 20/168 (11%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  N T++  R  F   G I S  + R K         S+GYGFV +   +  
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQ-----SLGYGFVNYIDPKDA 57

Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
            +A+  L    L    I++  +  +                    + + V  +P    Q 
Sbjct: 58  EKAINTLNGLRLQTKTIKVSYARPSSA--------------SIRDANLYVSGLPKTMTQK 103

Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
           E+E+LF  +G +   R+      +G+ RG GF+ F  + EA+ A+K L
Sbjct: 104 ELEQLFSQYGRIITSRILVDQ-VTGVSRGVGFIRFDKRIEAEEAIKGL 150

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 87.2 bits (217), Expect = 4e-20
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 33/188 (17%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + V  L   +T+++   LF   G +    L  DK T ++ G+  V ++ P+ A +A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 399 DGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYR 458
           +G     + + +   +P               S   +   N          + V  LP  
Sbjct: 65  NGLRLQTKTIKVSYARP---------------SSASIRDAN----------LYVSGLPKT 99

Query: 459 TLPTDLKALFEPFGDL--GRVLV-PPYGIT---GLVEFLQKNQAKAAFNSL--AYTKFKE 510
               +L+ LF  +G +   R+LV    G++   G + F ++ +A+ A   L         
Sbjct: 100 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT 159

Query: 511 VPLYLEWA 518
            P+ +++A
Sbjct: 160 EPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 69.9 bits (172), Expect = 4e-14
 Identities = 37/187 (19%), Positives = 75/187 (40%), Gaps = 44/187 (23%)

Query: 229 VKNLPAGVKKKDLKAYFKPL-PLASVR-----TTF--LGMAYIGFKDEKNCNKALNK-NK 279
           V  LP  + +++ ++ F  +  + S +      T   LG  ++ + D K+  KA+N  N 
Sbjct: 7   VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66

Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRI 339
              + K + +      + A+ S A+  + N                             +
Sbjct: 67  LRLQTKTIKV------SYARPSSASIRDAN-----------------------------L 91

Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
           +V  L  T+T+ +L +LF +YG +    + +D+ T  ++G   + F     A +A + L+
Sbjct: 92  YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151

Query: 400 GTVFLGR 406
           G    G 
Sbjct: 152 GQKPSGA 158

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 68.4 bits (168), Expect = 2e-13
 Identities = 37/214 (17%), Positives = 68/214 (31%), Gaps = 64/214 (29%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 499
           SK  ++V  LP      + ++LF   G++    +    ITG       V ++    A+ A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 500 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ 559
            N+L   + +   + + +A           S    ++ N                     
Sbjct: 61  INTLNGLRLQTKTIKVSYA---------RPSSASIRDAN--------------------- 90

Query: 560 QGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
                                  LY+  L    T+  + + F + G I +  +    D  
Sbjct: 91  -----------------------LYVSGLPKTMTQKELEQLFSQYGRIITSRILV--DQV 125

Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
           + G   S G GF++F  R    +A+K L      
Sbjct: 126 T-GV--SRGVGFIRFDKRIEAEEAIKGLNGQKPS 156

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 44.9 bits (107), Expect = 2e-05
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
            +TQE+ ++ F   G +   +L   K T  G+   + F+ Y     A+ A++  N   +
Sbjct: 12 QNMTQEEFRSLFGSIGEIESCKLVRDKIT--GQSLGYGFVNYIDPKDAEKAINTLNGLRL 69

Query: 84 FSSRIKV 90
           +  IKV
Sbjct: 70 QTKTIKV 76

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  105 bits (265), Expect = 4e-26
 Identities = 40/189 (21%), Positives = 76/189 (40%), Gaps = 21/189 (11%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
              P  +LY+ +L+ + TE  +   F   GPI S+ V R    +      S+GY +V F 
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR-----SLGYAYVNFQ 65

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPF 695
                 +AL  +    +    + +  S R              ++ K     I ++N+  
Sbjct: 66  QPADAERALDTMNFDVIKGKPVRIMWSQR------------DPSLRKSGVGNIFIKNLDK 113

Query: 696 QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY 755
                 + + F AFG +   ++   +      +G+GFV F T+  A+RA++ +     L 
Sbjct: 114 SIDNKALYDTFSAFGNILSCKV---VCDENGSKGYGFVHFETQEAAERAIEKM-NGMLLN 169

Query: 756 GRRLVLEWA 764
            R++ +   
Sbjct: 170 DRKVFVGRF 178

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 74.6 bits (184), Expect = 3e-15
 Identities = 46/240 (19%), Positives = 79/240 (32%), Gaps = 49/240 (20%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           +        ++V +L   VTE  L + F   GP+  + +  D  T ++ G+A V F  P 
Sbjct: 9   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRI 449
            A +A   ++  V  G+ + +                    S RK    N          
Sbjct: 69  DAERALDTMNFDVIKGKPVRI-------------MWSQRDPSLRKSGVGN---------- 105

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPP-----YGITGLVEFLQKNQAKAAFNS 502
           I +KNL        L   F  FG++   +V+        YG    V F  +  A+ A   
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF---VHFETQEAAERAIEK 162

Query: 503 LAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGV 562
           +      +  +++                   K + E E E G   K+    +  +  G 
Sbjct: 163 MNGMLLNDRKVFVGRF----------------KSRKEREAELGARAKEFYPYDVPDYAGS 206

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 71.2 bits (175), Expect = 4e-14
 Identities = 45/251 (17%), Positives = 77/251 (30%), Gaps = 64/251 (25%)

Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQ 492
           N    +     + V +L        L   F P G +  + V    IT        V F Q
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKEN 552
              A+ A +++ +   K  P+ + W+         ++     K                 
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWS---------QRDPSLRKSG--------------- 102

Query: 553 TAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 612
                                         ++IKNL+ +    ++   F   G I S  V
Sbjct: 103 ---------------------------VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 135

Query: 613 ARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT 672
               D        S GYGFV F T+E+  +A++ +    L++ ++ + R     E EA  
Sbjct: 136 VC--DENG-----SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 188

Query: 673 VKRKSSNVAKQ 683
             R        
Sbjct: 189 GARAKEFYPYD 199

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 10/75 (13%)

Query: 19 DLDEVEFIYKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAAL 75
          DL        +T+  L  KF   G +  +++     T   +   +A++ + +   A+ AL
Sbjct: 22 DLH-----PDVTEAMLYEKFSPAGPILSIRVCRDMIT--RRSLGYAYVNFQQPADAERAL 74

Query: 76 DYFNNTYVFSSRIKV 90
          D  N   +    +++
Sbjct: 75 DTMNFDVIKGKPVRI 89

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  103 bits (260), Expect = 6e-26
 Identities = 42/169 (24%), Positives = 78/169 (46%), Gaps = 22/169 (13%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           +    ++I  LN+++TED++R +F K G +  + +   KDP + G+  S G+GF+ F   
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKI--MKDPAT-GR--SRGFGFLSFEKP 55

Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA 697
            S+++ +K        +H ++     + ++      KR      +    KI V  I    
Sbjct: 56  SSVDEVVK-------TQHILD----GKVID-----PKRAIPRDEQDKTGKIFVGGIGPDV 99

Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           +  E EE F  +G +   +L      +G  RGFGFV + + +   R  +
Sbjct: 100 RPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVTYDSADAVDRVCQ 147

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 72.6 bits (179), Expect = 5e-15
 Identities = 29/146 (19%), Positives = 61/146 (41%), Gaps = 27/146 (18%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ES ++F+  L++  TED+L + F KYG + ++ +  D  T +++GF  ++F  P    + 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKN 454
            +            H++ GK       +D K           A  +  + ++ + I V  
Sbjct: 62  VK----------TQHILDGKV------IDPKR----------AIPRDEQDKTGK-IFVGG 94

Query: 455 LPYRTLPTDLKALFEPFGDLGRVLVP 480
           +     P + +  F  +G +    + 
Sbjct: 95  IGPDVRPKEFEEFFSQWGTIIDAQLM 120

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 70.6 bits (174), Expect = 2e-14
 Identities = 19/86 (22%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           ++  ++G+IFV  +   V   +  + F ++G + +  L +DK+T +++GF  VT+   + 
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPK 416
             +  Q      F  R + +   +P+
Sbjct: 142 VDRVCQ-NKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 53.3 bits (129), Expect = 2e-08
 Identities = 14/88 (15%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
            E +    +++  +  +         F + G I    +   KD          G+GFV +
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQS-----RGFGFVTY 136

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRS 662
            + +++++  +  +     + +IE+KR+
Sbjct: 137 DSADAVDRVCQ-NKFIDFKDRKIEIKRA 163

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 40.2 bits (95), Expect = 6e-04
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
           +  ++ +  F + GT+ D QL    + G+ R F F+ Y   D      
Sbjct: 99  VRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  100 bits (251), Expect = 2e-25
 Identities = 27/90 (30%), Positives = 43/90 (47%)

Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
           D+     + V NL+Y  + D L ++FEKYG + +V +P +  T   +GFA V F     A
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
             A   +DG    GR L +   +    + +
Sbjct: 69  QDAEAAMDGAELDGRELRVQVARYGRRDLS 98

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 75.0 bits (185), Expect = 1e-16
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
             SS         + V N+ ++     +  +F+ +G +  V +P++   +   RGF FV 
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH-TKAPRGFAFVR 61

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           F  + +A+ A  A+     L GR L ++ A  
Sbjct: 62  FHDRRDAQDAEAAM-DGAELDGRELRVQVARY 92

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 63.8 bits (156), Expect = 1e-12
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
            + +   TL + NL + ++ DS+RR F+K G +  V +   ++P +       G+ FV+F
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIP--REPHT-KA--PRGFAFVRF 62

Query: 635 YTRESLNQALKVLQNSSLDEHQI 657
           + R     A   +  + LD  ++
Sbjct: 63  HDRRDAQDAEAAMDGAELDGREL 85

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 51.5 bits (124), Expect = 3e-08
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
          Y+ + + L+  FE+ G V DV +    +T     R FAF+ +H    AQ A    +   +
Sbjct: 23 YRTSPDSLRRVFEKYGRVGDVYIPREPHT--KAPRGFAFVRFHDRRDAQDAEAAMDGAEL 80

Query: 84 FSSRIKVEK 92
              ++V+ 
Sbjct: 81 DGRELRVQV 89

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
           + V NL YRT P  L+ +FE +G +G V +P    T        V F  +  A+ A  ++
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 98.3 bits (245), Expect = 2e-24
 Identities = 29/88 (32%), Positives = 45/88 (51%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
            D+     + V NL+Y  + D L ++FEKYG + +V +P D+ T +++GFA V F     
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           A  A   +DG V  GR L +   +    
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYGRP 129

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 75.5 bits (186), Expect = 2e-16
 Identities = 23/120 (19%), Positives = 47/120 (39%), Gaps = 8/120 (6%)

Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
                 +    ++         +  + + V N+ ++     +  +F+ +G +  V +P+ 
Sbjct: 23  SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
              +   RGF FV F  K +A+ AM A+     L GR L ++ A         R   + +
Sbjct: 83  RY-TKESRGFAFVRFHDKRDAEDAMDAM-DGAVLDGRELRVQMARYG------RPPDSHH 134

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 60.9 bits (148), Expect = 3e-11
 Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
             + E  T+L + NL + ++ D++RR F+K G +  V + R  D  +  +  S G+ FV+
Sbjct: 41  PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR--DRYT-KE--SRGFAFVR 95

Query: 634 FYTRESLNQALKVLQNSSLDEHQI 657
           F+ +     A+  +  + LD  ++
Sbjct: 96  FHDKRDAEDAMDAMDGAVLDGREL 119

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 50.9 bits (122), Expect = 8e-08
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
           Y+ + + L+  FE+ G V DV +   +YT   + R FAF+ +H +  A+ A+D  +   +
Sbjct: 57  YRTSPDTLRRVFEKYGRVGDVYIPRDRYT--KESRGFAFVRFHDKRDAEDAMDAMDGAVL 114

Query: 84  FSSRIKVEK 92
               ++V+ 
Sbjct: 115 DGRELRVQM 123

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 45.1 bits (107), Expect = 7e-06
 Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
           + V NL YRT P  L+ +FE +G +G V +P    T        V F  K  A+ A +++
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 96.9 bits (242), Expect = 3e-24
 Identities = 35/90 (38%), Positives = 56/90 (62%), Gaps = 2/90 (2%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           + L+IKNLNF++TE++++  F K G I S T+   K     G  LSMG+GFV++   E  
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEA 670
            +ALK LQ  ++D H++E++ S R  +  +
Sbjct: 64  QKALKQLQGHTVDGHKLEVRISERATKPAS 93

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 80.8 bits (200), Expect = 9e-19
 Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT---KGFALVTFLMPEH 390
           + S  +F++NL+++ TE+ L  +F K G +    +   K         GF  V +  PE 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKE 417
           A +A + L G    G  L +   +   
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERAT 89

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 3/86 (3%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR--GFGFVEFITKNEAK 742
            S + ++N+ F   +  ++ +F   G +K   + KK   +G+    GFGFVE+    +A+
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 743 RAMKALCQSTHLYGRRLVLEWAEEAD 768
           +A+K L Q   + G +L +  +E A 
Sbjct: 65  KALKQL-QGHTVDGHKLEVRISERAT 89

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 4/68 (5%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR----FAFIGYHREDQAQAALDYFNNTY 82
          +  T+E LK  F + G +    +              F F+ Y + +QAQ AL       
Sbjct: 15 FSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT 74

Query: 83 VFSSRIKV 90
          V   +++V
Sbjct: 75 VDGHKLEV 82

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 94.9 bits (237), Expect = 8e-24
 Identities = 23/75 (30%), Positives = 36/75 (48%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           + S  +++R L    T+ DL KL + YG +      +DK T+K KG+  V F  P  A +
Sbjct: 3   SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

Query: 394 AYQHLDGTVFLGRML 408
           A   L  +    +M 
Sbjct: 63  AVTALKASGVQAQMA 77

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 58.7 bits (143), Expect = 4e-11
 Identities = 13/75 (17%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            S + +R +       ++ +L + +G++   +       +   +G+GFV+F + + A++A
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-TNKCKGYGFVDFDSPSAAQKA 63

Query: 745 MKALCQSTHLYGRRL 759
           + AL +++ +  +  
Sbjct: 64  VTAL-KASGVQAQMA 77

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
               + LYI+ L   +T+  + +  +  G I S       D  +  +    GYGFV F +
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAI--LDKTT-NK--CKGYGFVDFDS 56

Query: 637 RESLNQALKVLQNSSLD 653
             +  +A+  L+ S + 
Sbjct: 57  PSAAQKAVTALKASGVQ 73

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 44.4 bits (106), Expect = 5e-06
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 5/72 (6%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
             T + L    +  G +   +    K T   K + + F+ +     AQ A+     + V
Sbjct: 15 PGTTDQDLVKLCQPYGKIVSTKAILDKTT--NKCKGYGFVDFDSPSAAQKAVTALKASGV 72

Query: 84 FSSRIKVEKCSN 95
           +   K    S+
Sbjct: 73 QAQMAKQSGPSS 84

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 39.0 bits (92), Expect = 3e-04
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 6/58 (10%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
           ++ L   T   DL  L +P+G +          T        V+F   + A+ A  +L
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 97.2 bits (242), Expect = 1e-23
 Identities = 39/167 (23%), Positives = 59/167 (35%), Gaps = 21/167 (12%)

Query: 255 TTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMEN 314
            T  G       D     K   +              Y+ DN        DD        
Sbjct: 10  KTLKGETTTEAVDAATAEKVFKQ--------------YANDNGVDGEWTYDDATKTFTVT 55

Query: 315 IKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET 374
             + H            D+     + V NL+Y  + D L ++FEKYG + +V +P D+ T
Sbjct: 56  EGSHHHHH-------HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 108

Query: 375 DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
            +++GFA V F     A  A   +DG V  GR L +   +      +
Sbjct: 109 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 155

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 70.6 bits (173), Expect = 2e-14
 Identities = 25/140 (17%), Positives = 55/140 (39%), Gaps = 3/140 (2%)

Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGS 686
            G    +     +  +  K   N +  + +     + +   +          ++  +  +
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKT-FTVTEGSHHHHHHMDVEGMT 71

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V N+ ++     +  +F+ +G +  V +P+    +   RGF FV F  K +A+ AM 
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-TKESRGFAFVRFHDKRDAEDAMD 130

Query: 747 ALCQSTHLYGRRLVLEWAEE 766
           A+     L GR L ++ A  
Sbjct: 131 AM-DGAVLDGRELRVQMARY 149

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 67.9 bits (166), Expect = 2e-13
 Identities = 25/136 (18%), Positives = 55/136 (40%), Gaps = 5/136 (3%)

Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP 577
             + +  E   ++      +   +    +         +D  +     E +       + 
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           E  T+L + NL + ++ D++RR F+K G +  V + R  D  +  +  S G+ FV+F+ +
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR--DRYT-KE--SRGFAFVRFHDK 122

Query: 638 ESLNQALKVLQNSSLD 653
                A+  +  + LD
Sbjct: 123 RDAEDAMDAMDGAVLD 138

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 48.7 bits (116), Expect = 7e-07
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
           Y+ + + L+  FE+ G V DV +   +YT   + R FAF+ +H +  A+ A+D  +   +
Sbjct: 80  YRTSPDTLRRVFEKYGRVGDVYIPRDRYT--KESRGFAFVRFHDKRDAEDAMDAMDGAVL 137

Query: 84  FSSRIKVEK 92
               ++V+ 
Sbjct: 138 DGRELRVQM 146

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 43.7 bits (103), Expect = 4e-05
 Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
           + V NL YRT P  L+ +FE +G +G V +P    T        V F  K  A+ A +++
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 94.7 bits (236), Expect = 1e-23
 Identities = 18/87 (20%), Positives = 42/87 (48%), Gaps = 1/87 (1%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
            E  ++F+  L ++ T+++L ++ + +G + ++ L  ++   K KG A V +     A+Q
Sbjct: 15  LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQ 73

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEG 420
           A   +DG      ++ +       + G
Sbjct: 74  AVMKMDGMTIKENIIKVAISNSGPSSG 100

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 73.9 bits (182), Expect = 3e-16
 Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
             K+ +  +PF   + E+EE+ KA G +K +RL      +G  +G  +VE+  +++A +A
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR--AGKPKGLAYVEYENESQASQA 74

Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
           +  +     +    + +  +  
Sbjct: 75  VMKM-DGMTIKENIIKVAISNS 95

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 58.4 bits (142), Expect = 8e-11
 Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                   L+I  L F+ T++ +    K  G +  + +   +  K        G  +V++
Sbjct: 12  STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK------PKGLAYVEY 65

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSN 663
                 +QA+  +   ++ E+ I++  SN
Sbjct: 66  ENESQASQAVMKMDGMTIKENIIKVAISN 94

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 19/66 (28%), Positives = 33/66 (50%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          +  T+E+L+   +  GTV D++L     GK +  A++ Y  E QA  A+   +   +  +
Sbjct: 27 FSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKEN 86

Query: 87 RIKVEK 92
           IKV  
Sbjct: 87 IIKVAI 92

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 41.5 bits (98), Expect = 8e-05
 Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 7/64 (10%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAA 499
            K  + +  LP+     +L+ + +  G +  + +       P G+   VE+  ++QA  A
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL-AYVEYENESQASQA 74

Query: 500 FNSL 503
              +
Sbjct: 75  VMKM 78

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 95.6 bits (238), Expect = 2e-23
 Identities = 25/115 (21%), Positives = 42/115 (36%), Gaps = 1/115 (0%)

Query: 303 AADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGP 362
           A       S     A      +      +   +   ++V N+ Y  T  DL   F   G 
Sbjct: 3   APCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGS 62

Query: 363 LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
           +  + +  DK +   KG+A + F        A   +D TVF GR + ++P +   
Sbjct: 63  INRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRTNM 116

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 69.7 bits (171), Expect = 2e-14
 Identities = 25/130 (19%), Positives = 52/130 (40%), Gaps = 6/130 (4%)

Query: 545 GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC 604
                 + T  +       E        EE++     ++Y+ N+++ ST   +  HF  C
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 605 GPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
           G I  +T+   K    P      GY +++F  R S++ A+  +  +      I++     
Sbjct: 61  GSINRITILCDKFSGHP-----KGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRT 114

Query: 665 NLESEATTVK 674
           N+   ++T +
Sbjct: 115 NMPGISSTDR 124

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 60.1 bits (146), Expect = 4e-11
 Identities = 18/112 (16%), Positives = 43/112 (38%), Gaps = 5/112 (4%)

Query: 656 QIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFV 715
           Q    +      +E       +    +     + V N+ + +   ++E  F + G +  +
Sbjct: 7   QTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRI 66

Query: 716 RLPK-KMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
            +   K   SG  +G+ ++EF  +N    A+ A+ ++    GR + +     
Sbjct: 67  TILCDKF--SGHPKGYAYIEFAERNSVDAAV-AMDETV-FRGRTIKVLPKRT 114

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 6/63 (9%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
           +   KR + V N+ Y +   DL+A F   G + R+ +     +G       +EF ++N  
Sbjct: 32  KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91

Query: 497 KAA 499
            AA
Sbjct: 92  DAA 94

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
           Y  T + L+A F   G++  + +   K++  G  + +A+I +   +   AA+    +  V
Sbjct: 46  YGSTAQDLEAHFSSCGSINRITILCDKFS--GHPKGYAYIEFAERNSVDAAVAM--DETV 101

Query: 84  FSSR-IKV 90
           F  R IKV
Sbjct: 102 FRGRTIKV 109

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 94.7 bits (236), Expect = 2e-23
 Identities = 23/97 (23%), Positives = 44/97 (45%), Gaps = 6/97 (6%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
            D+ E   +F+RNLS+   E+ L ++ +++G L  V + +  +T+ +KG A   F+  E 
Sbjct: 10  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69

Query: 391 ATQAYQHLD------GTVFLGRMLHLIPGKPKENEGN 421
           A +            G    GR L +     ++   +
Sbjct: 70  AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 76.2 bits (188), Expect = 6e-17
 Identities = 24/100 (24%), Positives = 48/100 (48%), Gaps = 8/100 (8%)

Query: 674 KRKSSNVAK--QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 731
              SS +      G  + +RN+ F +++  + E+ + FG+LK+VR+      +   +G  
Sbjct: 2   SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-TEHSKGCA 60

Query: 732 FVEFITKNEAKRAMKALCQSTH-----LYGRRLVLEWAEE 766
           F +F+T+  A++ + A           L GR+L ++ A  
Sbjct: 61  FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 64.7 bits (158), Expect = 7e-13
 Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
                 +     T++I+NL+F+S E+++    ++ G +  V V     P +     S G 
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV--LHPDT-EH--SKGC 59

Query: 630 GFVQFYTRESLNQALKVLQNSS 651
            F QF T+E+  + L      +
Sbjct: 60  AFAQFMTQEAAQKCLAAASLEA 81

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 41.6 bits (98), Expect = 9e-05
 Identities = 9/56 (16%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNT 81
          +   +E L    ++ G +  V++    +    +  AF  +  ++ AQ  L   +  
Sbjct: 25 FDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLE 80

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 40.0 bits (94), Expect = 3e-04
 Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
           +    + + ++NL + +    L  + + FGDL  V V  +  T         +F+ +  A
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70

Query: 497 KAAFNSL 503
           +    + 
Sbjct: 71  QKCLAAA 77

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 95.7 bits (238), Expect = 4e-23
 Identities = 25/121 (20%), Positives = 56/121 (46%), Gaps = 3/121 (2%)

Query: 304 ADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPL 363
           +D N   ++ + +    +  ++     +   E   +FV ++     ED++ + F  YG +
Sbjct: 40  SDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEI 99

Query: 364 AEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL---IPGKPKENEG 420
             + L +D+ T  +KG+ALV +   + A  A + L+G   +G+ + +       PK  + 
Sbjct: 100 KNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKK 159

Query: 421 N 421
           +
Sbjct: 160 S 160

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 72.6 bits (178), Expect = 5e-15
 Identities = 28/131 (21%), Positives = 56/131 (42%), Gaps = 7/131 (5%)

Query: 649 NSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKA 708
           +S+  E     +R     + E     ++S       G  + V +I  +A++ E++E F  
Sbjct: 41  DSNTREAIHSYERVRNEDDDELEPGPQRSV-----EGWILFVTSIHEEAQEDEIQEKFCD 95

Query: 709 FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD 768
           +GE+K + L      +G  +G+  VE+ T  +A  A +AL     + G+ + ++W     
Sbjct: 96  YGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAAKEAL-NGAEIMGQTIQVDWCFVKG 153

Query: 769 NVEDIRKRTNR 779
                +    R
Sbjct: 154 PKRVKKSEKRR 164

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 64.9 bits (158), Expect = 2e-12
 Identities = 26/143 (18%), Positives = 56/143 (39%), Gaps = 5/143 (3%)

Query: 515 LEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
           ++ A E    E  ++   + KEK +     G            + + V   +++  E   
Sbjct: 7   IDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGP 66

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +       L++ +++  + ED I+  F   G I ++ +    D ++ G   S GY  V++
Sbjct: 67  QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL--DRRT-GF--SKGYALVEY 121

Query: 635 YTRESLNQALKVLQNSSLDEHQI 657
            T +    A + L  + +    I
Sbjct: 122 ETHKQALAAKEALNGAEIMGQTI 144

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 51.4 bits (123), Expect = 1e-07
 Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            +  +++++ KF + G + ++ L      G  + +A + Y    QA AA +  N   +  
Sbjct: 82  EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 141

Query: 86  SRIKVEKC 93
             I+V+ C
Sbjct: 142 QTIQVDWC 149

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 42.5 bits (100), Expect = 1e-04
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
           I+ V ++       +++  F  +G++  + +     TG      LVE+    QA AA  +
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 503 LAYTKFKEVPLYLEWA 518
           L   +     + ++W 
Sbjct: 134 LNGAEIMGQTIQVDWC 149

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 92.3 bits (230), Expect = 1e-22
 Identities = 30/94 (31%), Positives = 47/94 (50%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
               ++  I V NLS    E DL +LF  +G ++ + L  DK T ++KGFA ++F   E 
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDG 424
           A +A   + G  +   +L++   KP  N G   G
Sbjct: 70  AARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 73.4 bits (181), Expect = 5e-16
 Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            + I V N+    ++++++ELF+ FG +  + L K    +G  +GF F+ F  + +A RA
Sbjct: 15  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-TGQSKGFAFISFHRREDAARA 73

Query: 745 MKALCQSTHLYGRRLVLEWAEEADN 769
           +  +          L +EWA+ + N
Sbjct: 74  IAGV-SGFGYDHLILNVEWAKPSTN 97

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 63.4 bits (155), Expect = 2e-12
 Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           R  + + T+ + NL+ ++ E  ++  F+  G I+ + +A+  D  + GQ  S G+ F+ F
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAK--DKTT-GQ--SKGFAFISF 64

Query: 635 YTRESLNQALKVLQNSSLD 653
           + RE   +A+  +     D
Sbjct: 65  HRREDAARAIAGVSGFGYD 83

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
              +  L+  F   G+++ + L   K T  G+ + FAFI +HR + A  A+   +    
Sbjct: 25 EDTRETDLQELFRPFGSISRIYLAKDKTT--GQSKGFAFISFHRREDAARAIAGVSGFGY 82

Query: 84 FSSRIKVEK 92
              + VE 
Sbjct: 83 DHLILNVEW 91

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
           I V NL   T  TDL+ LF PFG + R+ +     TG       + F ++  A  A   +
Sbjct: 18  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77

Query: 504 AYTKFKEVPLYLEWA 518
           +   +  + L +EWA
Sbjct: 78  SGFGYDHLILNVEWA 92

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 91.7 bits (228), Expect = 2e-22
 Identities = 20/72 (27%), Positives = 32/72 (44%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +    L+  V E  L  +  KYG + EV + +   T K  G A V F     A +  ++
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 398 LDGTVFLGRMLH 409
           L  T  +G ++H
Sbjct: 68  LHLTSVMGNIIH 79

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 70.1 bits (172), Expect = 8e-15
 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 5/81 (6%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
             P   +    LN N  E  ++   +K G +  V +      +       +G   V F +
Sbjct: 3   QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRK-----HLGLARVLFTS 57

Query: 637 RESLNQALKVLQNSSLDEHQI 657
                + +K L  +S+  + I
Sbjct: 58  TRGAKETVKNLHLTSVMGNII 78

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 60.1 bits (146), Expect = 3e-11
 Identities = 13/75 (17%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
             ++    +    +++ ++++ + +GE++ V +      +  H G   V F +   AK  
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR-TRKHLGLARVLFTSTRGAKET 64

Query: 745 MKALCQSTHLYGRRL 759
           +K L   T + G  +
Sbjct: 65  VKNL-HLTSVMGNII 78

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 13/87 (14%), Positives = 30/87 (34%), Gaps = 9/87 (10%)

Query: 7  GPVVPRN-HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIG 64
          G +  +    + L+         + +  LK    + G V +V++       K    A + 
Sbjct: 2  GQIPLKEVTFARLN-------DNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVL 54

Query: 65 YHREDQAQAALDYFNNTYVFSSRIKVE 91
          +     A+  +   + T V  + I  +
Sbjct: 55 FTSTRGAKETVKNLHLTSVMGNIIHAQ 81

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAF 500
            + +    L      T LK +   +G++  V +  +  T        V F     AK   
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 501 NSLAYTKFKEVPLYLEWAPEG 521
            +L  T      ++ +   +G
Sbjct: 66  KNLHLTSVMGNIIHAQLDIKG 86

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 90.3 bits (225), Expect = 5e-22
 Identities = 25/88 (28%), Positives = 49/88 (55%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           + S  ++V +L + +TED L  +FE +G +  ++L  D +T ++KG+  +TF   E A +
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
           A + L+G    GR + +     + + G+
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDGGS 90

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 69.1 bits (170), Expect = 1e-14
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S + V ++ F   +  +  +F+ FG++  + L K    +G  +G+GF+ F     A+RA+
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD-TGRSKGYGFITFSDSECARRAL 64

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
           + L     L GR + +    E
Sbjct: 65  EQL-NGFELAGRPMRVGHVTE 84

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
              + LY+ +L+FN TED +R  F+  G I ++ +   KD  + G+  S GYGF+ F   
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLM--KDSDT-GR--SKGYGFITFSDS 57

Query: 638 ESLNQALKVLQNSSLD 653
           E   +AL+ L    L 
Sbjct: 58  ECARRALEQLNGFELA 73

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 15/65 (23%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          + IT++ L+  FE  G + ++ L   ++ G+ + + FI +   + A+ AL+  N   +  
Sbjct: 15 FNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG 74

Query: 86 SRIKV 90
            ++V
Sbjct: 75 RPMRV 79

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 38.3 bits (90), Expect = 7e-04
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 6/60 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
           + V +L +      L+ +FEPFG +  +++     TG       + F     A+ A   L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 89.2 bits (222), Expect = 1e-21
 Identities = 25/73 (34%), Positives = 43/73 (58%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           +  + V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 396 QHLDGTVFLGRML 408
           +  +G    GR +
Sbjct: 75  ERANGMELDGRRI 87

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 2/90 (2%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
              +         + V  +     + ++ E+F  +G +  V +      S   RGF FV 
Sbjct: 5   SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRRSRGFAFVY 63

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
           F   ++AK A +       L GRR+ +   
Sbjct: 64  FENVDDAKEAKERANGME-LDGRRIRVSGP 92

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
            P+P+  L +  L+  +TE  +R  F K GPIA V++    D +S  +  S G+ FV F 
Sbjct: 11  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV--YDQQS-RR--SRGFAFVYFE 65

Query: 636 TRESLNQALKVLQNSSLDEHQI 657
             +   +A +      LD  +I
Sbjct: 66  NVDDAKEAKERANGMELDGRRI 87

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 49.9 bits (120), Expect = 6e-08
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
             T+  L+  F + G + DV + Y  +  + R FAF+ +   D A+ A +  N   +  
Sbjct: 25 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 84

Query: 86 SRIKVEK 92
           RI+V  
Sbjct: 85 RRIRVSG 91

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
           + V  L   T   DL+ +F  +G +  V +     +        V F   + AK A    
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 88.9 bits (221), Expect = 1e-21
 Identities = 26/88 (29%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           +   +  R+FV NL   +TE+++ KLFEKYG   EV +  D      KGF  +       
Sbjct: 10  KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTL 63

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           A  A   LD     G+ L +       +
Sbjct: 64  AEIAKVELDNMPLRGKQLRVRFACHSAS 91

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 73.8 bits (182), Expect = 3e-16
 Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 8/87 (9%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            S++ V N+P    + E+ +LF+ +G+   V + K        +GFGF+   T+  A+ A
Sbjct: 15  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-------DKGFGFIRLETRTLAEIA 67

Query: 745 MKALCQSTHLYGRRLVLEWAEEADNVE 771
              L  +  L G++L + +A  + ++ 
Sbjct: 68  KVEL-DNMPLRGKQLRVRFACHSASLT 93

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 11/93 (11%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
             E+     + L++ NL  + TE+ +R+ F+K G    V + + K           G+GF
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----------GFGF 55

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
           ++  TR     A   L N  L   Q+ ++ +  
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFACH 88

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYT 506
           + V NLP      +++ LFE +G  G V +     +   G +    +  A+ A   L   
Sbjct: 18  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGF---GFIRLETRTLAEIAKVELDNM 74

Query: 507 KFKEVPLYLEWAPEG 521
             +   L + +A   
Sbjct: 75  PLRGKQLRVRFACHS 89

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 44.6 bits (106), Expect = 6e-06
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 5/65 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            IT+E+++  FE+ G   +V +      K + F FI       A+ A    +N  +   
Sbjct: 25 PDITEEEMRKLFEKYGKAGEVFIH-----KDKGFGFIRLETRTLAEIAKVELDNMPLRGK 79

Query: 87 RIKVE 91
          +++V 
Sbjct: 80 QLRVR 84

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 89.8 bits (223), Expect = 2e-21
 Identities = 25/73 (34%), Positives = 43/73 (58%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           +  + V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A 
Sbjct: 46  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105

Query: 396 QHLDGTVFLGRML 408
           +  +G    GR +
Sbjct: 106 ERANGMELDGRRI 118

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 69.8 bits (171), Expect = 2e-14
 Identities = 20/106 (18%), Positives = 40/106 (37%), Gaps = 2/106 (1%)

Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
            S    +      +   +         + V  +     + ++ E+F  +G +  V +   
Sbjct: 22  ASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 81

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
              S   RGF FV F   ++AK A +       L GRR+ ++++  
Sbjct: 82  QQ-SRRSRGFAFVYFENVDDAKEAKERA-NGMELDGRRIRVDFSIT 125

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 69.0 bits (169), Expect = 4e-14
 Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
                  P+P+  L +  L+  +TE  +R  F K GPIA V++    D +S  +  S G+
Sbjct: 36  HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY--DQQS-RR--SRGF 90

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQI 657
            FV F   +   +A +      LD  +I
Sbjct: 91  AFVYFENVDDAKEAKERANGMELDGRRI 118

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 49.7 bits (119), Expect = 2e-07
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
              T+  L+  F + G + DV +   + +   + R FAF+ +   D A+ A +  N   +
Sbjct: 56  LYTTERDLREVFSKYGPIADVSIVYDQQS--RRSRGFAFVYFENVDDAKEAKERANGMEL 113

Query: 84  FSSRIKVEK 92
              RI+V+ 
Sbjct: 114 DGRRIRVDF 122

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 42.0 bits (99), Expect = 9e-05
 Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 6/64 (9%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAA 499
               + V  L   T   DL+ +F  +G +  V +     +        V F   + AK A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 500 FNSL 503
               
Sbjct: 105 KERA 108

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 88.8 bits (221), Expect = 2e-21
 Identities = 26/85 (30%), Positives = 47/85 (55%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           ++ G++FV  LS+   E  L ++F KYG ++EV++  D+ET +++GF  VTF   + A  
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
           A   ++G    GR + +       +
Sbjct: 70  AMMAMNGKSVDGRQIRVDQAGKSSD 94

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 66.1 bits (162), Expect = 2e-13
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            K+ V  + F   +  +E++F  +G++  V + K    +   RGFGFV F   ++AK AM
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-TQRSRGFGFVTFENIDDAKDAM 71

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
            A+     + GR++ ++ A +
Sbjct: 72  MAM-NGKSVDGRQIRVDQAGK 91

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.4 bits (155), Expect = 2e-12
 Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 5/88 (5%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
               +  L++  L+F++ E S+ + F K G I+ V V   KD ++  +  S G+GFV F 
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVV--KDRET-QR--SRGFGFVTFE 62

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSN 663
             +    A+  +   S+D  QI + ++ 
Sbjct: 63  NIDDAKDAMMAMNGKSVDGRQIRVDQAG 90

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
          +   ++ L+  F + G +++V +   + T   + R F F+ +   D A+ A+   N   V
Sbjct: 22 FDTNEQSLEQVFSKYGQISEVVVVKDRET--QRSRGFGFVTFENIDDAKDAMMAMNGKSV 79

Query: 84 FSSRIKVEK 92
             +I+V++
Sbjct: 80 DGRQIRVDQ 88

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 88.0 bits (219), Expect = 3e-21
 Identities = 23/73 (31%), Positives = 43/73 (58%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
              ++V NL +++T +DL ++F KYG + +V +  DK+T K+KG A + FL  + A    
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75

Query: 396 QHLDGTVFLGRML 408
           + ++     GR++
Sbjct: 76  RAINNKQLFGRVI 88

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 66.5 bits (163), Expect = 1e-13
 Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           + S + V N+PF    +++  +F  +G++  V + K    +   +G  F+ F+ K+ A+ 
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK-DTRKSKGVAFILFLDKDSAQN 73

Query: 744 AMKALCQSTHLYGRRLVLEWA 764
             +A+  +  L+GR +    A
Sbjct: 74  CTRAI-NNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
                +T+Y+ NL F+ T + + R F K G +  VT+ + KD     +  S G  F+ F 
Sbjct: 12  LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD---TRK--SKGVAFILFL 66

Query: 636 TRESLNQALKVLQNSSLD 653
            ++S     + + N  L 
Sbjct: 67  DKDSAQNCTRAINNKQLF 84

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
          + +T   L   F + G V  V +   K T   K +  AFI +  +D AQ      NN  +
Sbjct: 26 FSLTNNDLYRIFSKYGKVVKVTIMKDKDT--RKSKGVAFILFLDKDSAQNCTRAINNKQL 83

Query: 84 FSSRIKVEK 92
          F   IK   
Sbjct: 84 FGRVIKASI 92

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 41.4 bits (98), Expect = 6e-05
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 6/67 (8%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 496
            A SK  + V NLP+     DL  +F  +G + +V +     T        + FL K+ A
Sbjct: 12  LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71

Query: 497 KAAFNSL 503
           +    ++
Sbjct: 72  QNCTRAI 78

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 89.5 bits (222), Expect = 4e-21
 Identities = 23/98 (23%), Positives = 48/98 (48%)

Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
             + D+ +  + + +S  ++V NLS+  TE+ + +LF K G + ++I+ +DK      GF
Sbjct: 24  HFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGF 83

Query: 381 ALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
             V +     A  A ++++GT    R++        + 
Sbjct: 84  CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 121

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 76.4 bits (188), Expect = 2e-16
 Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 5/87 (5%)

Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
           E++E+  +   TLY+ NL+F +TE+ I   F K G I  + +   K  K+       G+ 
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA-----CGFC 84

Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQI 657
           FV++Y+R     A++ +  + LD+  I
Sbjct: 85  FVEYYSRADAENAMRYINGTRLDDRII 111

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 71.0 bits (174), Expect = 1e-14
 Identities = 22/108 (20%), Positives = 45/108 (41%), Gaps = 10/108 (9%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
            +      +    + V N+ F   + ++ ELF   G++K + +    +      GF FVE
Sbjct: 29  NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KKTACGFCFVE 87

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
           + ++ +A+ AM+ +   T L  R +  +W            +  R +G
Sbjct: 88  YYSRADAENAMRYI-NGTRLDDRIIRTDWDA--------GFKEGRQYG 126

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 51.7 bits (124), Expect = 7e-08
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           +  T+EQ+   F + G +  + +           F F+ Y+    A+ A+ Y N T +  
Sbjct: 49  FYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD 108

Query: 86  SRIKVEK 92
             I+ + 
Sbjct: 109 RIIRTDW 115

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 49.4 bits (118), Expect = 4e-07
 Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 6/95 (6%)

Query: 431 SERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--- 487
              + D   Q    +    + V NL + T    +  LF   GD+ ++++    +      
Sbjct: 23  QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82

Query: 488 ---VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP 519
              VE+  +  A+ A   +  T+  +  +  +W  
Sbjct: 83  FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 87.7 bits (218), Expect = 5e-21
 Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 8/95 (8%)

Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
                  E    + R+FVR     V E +L ++F  +GP+ EV +          GFA V
Sbjct: 19  SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFV 70

Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            F   E A +A + + G  F  + L ++  K    
Sbjct: 71  EFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 68.9 bits (169), Expect = 2e-14
 Identities = 22/117 (18%), Positives = 45/117 (38%), Gaps = 14/117 (11%)

Query: 660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK 719
              + +                + + +++ VR  P   ++SE+ E+F  FG +K V++  
Sbjct: 6   HHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN 65

Query: 720 KMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKR 776
                    GF FVEF     A +A++ +        + L + +++        R R
Sbjct: 66  ---------GFAFVEFEEAESAAKAIEEV-HGKSFANQPLEVVYSKLPAK----RYR 108

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 61.5 bits (150), Expect = 9e-12
 Identities = 17/95 (17%), Positives = 34/95 (35%), Gaps = 13/95 (13%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
               +     +T L+++    +  E  +   F   GP+  V +               G+
Sbjct: 21  MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------------GF 67

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
            FV+F   ES  +A++ +   S     +E+  S  
Sbjct: 68  AFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL 102

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 45.7 bits (109), Expect = 3e-06
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
           + V+  P     ++L  +F PFG +  V +   G    VEF +   A  A   +    F 
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-G-FAFVEFEEAESAAKAIEEVHGKSFA 91

Query: 510 EVPLYLEWA 518
             PL + ++
Sbjct: 92  NQPLEVVYS 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 41.5 bits (98), Expect = 8e-05
 Identities = 10/65 (15%), Positives = 26/65 (40%), Gaps = 7/65 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            + + +L   F   G + +V++          FAF+ +   + A  A++  +     + 
Sbjct: 41 LDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQ 93

Query: 87 RIKVE 91
           ++V 
Sbjct: 94 PLEVV 98

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 86.4 bits (215), Expect = 8e-21
 Identities = 20/85 (23%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK-ETDKTKGFALVTFLMPEHATQ 393
           +  ++ +  L+  VT+D + ++F  YG +  + +P+++     +KG+A V F  P+ A +
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
           A +H+DG    G+ +          
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWP 87

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 73.3 bits (181), Expect = 3e-16
 Identities = 17/94 (18%), Positives = 43/94 (45%), Gaps = 10/94 (10%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           +K+ +  +     +  + E+F  +G++K + +P + +   L +G+ +VEF   +EA++A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 746 KALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
           K +     + G+ +             +     R
Sbjct: 65  KHM-DGGQIDGQEI---------TATAVLAPWPR 88

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
             T ++I  L  N T+D I   F   G I  + +    +   P    S GY +V+F   +
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMP--VERMHPHL--SKGYAYVEFENPD 58

Query: 639 SLNQALKVLQNSSLDEHQI 657
              +ALK +    +D  +I
Sbjct: 59  EAEKALKHMDGGQIDGQEI 77

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 49.8 bits (120), Expect = 7e-08
 Identities = 9/69 (13%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
            +T++ +   F   G +  + +   +       + +A++ +   D+A+ AL + +   +
Sbjct: 14 RNVTKDHIMEIFSTYGKIKMIDMPVERMHP-HLSKGYAYVEFENPDEAEKALKHMDGGQI 72

Query: 84 FSSRIKVEK 92
              I    
Sbjct: 73 DGQEITATA 81

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 87.0 bits (216), Expect = 1e-20
 Identities = 21/99 (21%), Positives = 48/99 (48%)

Query: 311 SMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPI 370
           ++ + +    +  ++     +   E   +FV ++     ED++ + F  YG +  + L +
Sbjct: 1   AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60

Query: 371 DKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH 409
           D+ T  +KG+ALV +   + A  A + L+G   +G+ + 
Sbjct: 61  DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 99

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 71.9 bits (177), Expect = 2e-15
 Identities = 27/113 (23%), Positives = 51/113 (45%), Gaps = 9/113 (7%)

Query: 654 EHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK 713
            H  E  R+  + E E    +          G  + V +I  +A++ E++E F  +GE+K
Sbjct: 2   IHSYERVRNEDDDELEPGPQRSVE-------GWILFVTSIHEEAQEDEIQEKFCDYGEIK 54

Query: 714 FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
            + L      +G  +G+  VE+ T  +A  A +AL     + G+ + ++W   
Sbjct: 55  NIHLNLDR-RTGFSKGYALVEYETHKQALAAKEAL-NGAEIMGQTIQVDWCFV 105

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 53.8 bits (130), Expect = 4e-09
 Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 12/98 (12%)

Query: 567 ENVEEDEEREPEPDT-------TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
           E V  +++ E EP          L++ +++  + ED I+  F   G I ++ +    D +
Sbjct: 6   ERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL--DRR 63

Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
           + G   S GY  V++ T +    A + L  + +    I
Sbjct: 64  T-GF--SKGYALVEYETHKQALAAKEALNGAEIMGQTI 98

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 51.5 bits (124), Expect = 3e-08
 Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            +  +++++ KF + G + ++ L      G  + +A + Y    QA AA +  N   +  
Sbjct: 36  EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 95

Query: 86  SRIKVEKC 93
             I+V+ C
Sbjct: 96  QTIQVDWC 103

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
           I+ V ++       +++  F  +G++  + +     TG      LVE+    QA AA  +
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 503 LAYTKFKEVPLYLEWA 518
           L   +     + ++W 
Sbjct: 88  LNGAEIMGQTIQVDWC 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 86.5 bits (215), Expect = 1e-20
 Identities = 21/76 (27%), Positives = 39/76 (51%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           E   +FV  +    TE+D+   F +YG +  + L +D+ T   KG+ LV +   + A  A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 395 YQHLDGTVFLGRMLHL 410
            + L+G   +G+ + +
Sbjct: 82  MEGLNGQDLMGQPISV 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 73.1 bits (180), Expect = 8e-16
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G  + V  +  +A + ++ + F  +GE+K + L      +G  +G+  VE+ T  EA+ A
Sbjct: 23  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 81

Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
           M+ L     L G+ + ++W   
Sbjct: 82  MEGL-NGQDLMGQPISVDWCFV 102

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            + T+E +  KF E G + ++ L      G  + +  + Y    +AQAA++  N   +  
Sbjct: 33  EEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 92

Query: 86  SRIKVEKC 93
             I V+ C
Sbjct: 93  QPISVDWC 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 10/99 (10%)

Query: 564 EVEENVEEDEEREPEPD-----TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP 618
             + +  E +  EP P        L++  ++  +TE+ I   F + G I ++ +    D 
Sbjct: 2   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL--DR 59

Query: 619 KSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
           ++ G     GY  V++ T +    A++ L    L    I
Sbjct: 60  RT-GY--LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 95

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
           I+ V  +       D+   F  +G++  + +     TG      LVE+    +A+AA   
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 503 LAYTKFKEVPLYLEWA 518
           L        P+ ++W 
Sbjct: 85  LNGQDLMGQPISVDWC 100

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 86.6 bits (215), Expect = 1e-20
 Identities = 26/91 (28%), Positives = 48/91 (52%)

Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
              +  A   R++V +L + +TED L  +FE +G +  + L +D ET ++KG+  +TF  
Sbjct: 18  NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77

Query: 388 PEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            E A +A + L+G    GR + +     + +
Sbjct: 78  SECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 68.5 bits (168), Expect = 3e-14
 Identities = 21/109 (19%), Positives = 49/109 (44%), Gaps = 7/109 (6%)

Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
             +    + A  +++ S+        ++ V ++ F   +  +  +F+ FG ++ ++L   
Sbjct: 7   HHSHMAAAMANNLQKGSAG-----PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
              +G  +G+GF+ F     AK+A++ L     L GR + +    E  +
Sbjct: 62  SE-TGRSKGYGFITFSDSECAKKALEQL-NGFELAGRPMKVGHVTERTD 108

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 56.9 bits (138), Expect = 3e-10
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
           ++       LY+ +L+FN TED +R  F+  G I S+ +    D ++ G+  S GYGF+ 
Sbjct: 20  QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLM--MDSET-GR--SKGYGFIT 74

Query: 634 FYTRESLNQALKVLQNSSLD 653
           F   E   +AL+ L    L 
Sbjct: 75  FSDSECAKKALEQLNGFELA 94

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           + IT++ L+  FE  G +  +QL   +E G+ + + FI +   + A+ AL+  N   +  
Sbjct: 36  FNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG 95

Query: 86  SRIKV 90
             +KV
Sbjct: 96  RPMKV 100

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 6/60 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
           + V +L +      L+ +FEPFG +  + +     TG       + F     AK A   L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 85.6 bits (213), Expect = 2e-20
 Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           A++  I+V N+ Y  T ++L   F   G +  V +  DK +   KGFA + F   E    
Sbjct: 4   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKE 417
           +   LD ++F GR + +IP +   
Sbjct: 64  SLA-LDESLFRGRQIKVIPKRTNR 86

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 64.1 bits (157), Expect = 6e-13
 Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 14/92 (15%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD---PKSPGQFLSMGYGFVQF 634
               ++Y+ N+++ +T + +  HF  CG +  VT+   K    PK        G+ +++F
Sbjct: 4   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPK--------GFAYIEF 55

Query: 635 YTRESLNQALKVLQNSSLDEHQI--ELKRSNR 664
             +ES+  +L  L  S     QI    KR+NR
Sbjct: 56  SDKESVRTSLA-LDESLFRGRQIKVIPKRTNR 86

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 60.6 bits (148), Expect = 1e-11
 Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAM 745
            I V N+ + A   E+E  F   G +  V +   K   SG  +GF ++EF  K   + ++
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF--SGHPKGFAYIEFSDKESVRTSL 65

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
            AL +S    GR++ +     
Sbjct: 66  -ALDESL-FRGRQIKVIPKRT 84

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 43.7 bits (104), Expect = 1e-05
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 9/74 (12%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
          Y  T E+L+A F   G+V  V +   K++  G  + FA+I +  ++  + +L    +  +
Sbjct: 16 YGATAEELEAHFHGCGSVNRVTILCDKFS--GHPKGFAYIEFSDKESVRTSLAL--DESL 71

Query: 84 FSSR-IKV-EKCSN 95
          F  R IKV  K +N
Sbjct: 72 FRGRQIKVIPKRTN 85

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 41.7 bits (99), Expect = 5e-05
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 6/61 (9%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKA 498
              R I V N+ Y     +L+A F   G + RV +     +G       +EF  K   + 
Sbjct: 4   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 499 A 499
           +
Sbjct: 64  S 64

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 85.4 bits (212), Expect = 2e-20
 Identities = 20/86 (23%), Positives = 40/86 (46%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S  +++ ++ Y  TE+ +  L    GP+  + +  D +T ++KG+A + F   E +  A 
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGN 421
           ++L+G     R L        +  G 
Sbjct: 62  RNLNGYQLGSRFLKCGYSSNSDISGV 87

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 68.0 bits (167), Expect = 3e-14
 Identities = 15/95 (15%), Positives = 40/95 (42%), Gaps = 2/95 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
             + + +IP+   + ++ +L    G +  +++      +G  +G+ F+EF     +  A+
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-TGRSKGYAFIEFRDLESSASAV 61

Query: 746 KALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
           + L     L  R L   ++  +D      +  + +
Sbjct: 62  RNL-NGYQLGSRFLKCGYSSNSDISGVSLEHHHHH 95

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 56.1 bits (136), Expect = 5e-10
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
           P   +Y+ ++ ++ TE+ I       GP+ ++ +    DP++ G+  S GY F++F   E
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF--DPQT-GR--SKGYAFIEFRDLE 55

Query: 639 SLNQALKVLQNSSLDEHQI 657
           S   A++ L    L    +
Sbjct: 56  SSASAVRNLNGYQLGSRFL 74

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 49.9 bits (120), Expect = 7e-08
 Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           Y  T+EQ+       G V ++++ +  + G+ + +AFI +   + + +A+   N   + S
Sbjct: 12  YDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS 71

Query: 86  SRIKVEKCSNLGDTTKPKSWSKY 108
             +K    SN   +        +
Sbjct: 72  RFLKCGYSSNSDISGVSLEHHHH 94

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 86.8 bits (215), Expect = 3e-20
 Identities = 22/100 (22%), Positives = 41/100 (41%), Gaps = 1/100 (1%)

Query: 309 NASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVIL 368
                  +     S                ++V  L+  V +  L   F  +G + ++ +
Sbjct: 37  TCVNCTERHVDGGSGGSGGSGGSA-TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95

Query: 369 PIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRML 408
           P+D ET+K +GFA V F + E A  A  +++ +   GR +
Sbjct: 96  PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 76.0 bits (187), Expect = 2e-16
 Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 2/104 (1%)

Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
            +      +  +     S  +  T   + V  +  +     +   F  FG++  +++P  
Sbjct: 39  VNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 98

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
              +  HRGF FVEF    +A  A+  + +S  L+GR + +  A
Sbjct: 99  YE-TEKHRGFAFVEFELAEDAAAAIDNMNESE-LFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 60.2 bits (146), Expect = 5e-11
 Identities = 15/100 (15%), Positives = 30/100 (30%), Gaps = 5/100 (5%)

Query: 554 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 613
              +  +   +                  LY+  L     +  +   F   G I  + + 
Sbjct: 37  TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP 96

Query: 614 RKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
              D ++  +    G+ FV+F   E    A+  +  S L 
Sbjct: 97  --LDYET-EK--HRGFAFVEFELAEDAAAAIDNMNESELF 131

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 49.8 bits (119), Expect = 2e-07
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            ++  + L A F   G +TD+Q+    E  K R FAF+ +   + A AA+D  N + +F 
Sbjct: 73  EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 132

Query: 86  SRIKVEK 92
             I+V  
Sbjct: 133 RTIRVNL 139

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
            A +KR++ V  L        L A F PFGD+  + +P    T        VEF     A
Sbjct: 59  SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118

Query: 497 KAAFNSL 503
            AA +++
Sbjct: 119 AAAIDNM 125

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 85.3 bits (212), Expect = 3e-20
 Identities = 23/88 (26%), Positives = 44/88 (50%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
                ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A  
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
           A  +++ +   GR + +   KP   + +
Sbjct: 70  AIDNMNESELFGRTIRVNLAKPMRIKES 97

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 71.1 bits (175), Expect = 3e-15
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
             + V  +  +     +   F  FG++  +++P     +  HRGF FVEF    +A  A+
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAAAAI 71

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
             +   + L+GR + +  A+ 
Sbjct: 72  DNM-NESELFGRTIRVNLAKP 91

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 5/76 (6%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
                LY+  L     +  +   F   G I  + +    D ++  +    G+ FV+F   
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP--LDYET-EK--HRGFAFVEFELA 64

Query: 638 ESLNQALKVLQNSSLD 653
           E    A+  +  S L 
Sbjct: 65  EDAAAAIDNMNESELF 80

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           ++  + L A F   G +TD+Q+    E  K R FAF+ +   + A AA+D  N + +F 
Sbjct: 22 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 81

Query: 86 SRIKVEK 92
            I+V  
Sbjct: 82 RTIRVNL 88

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 43.7 bits (104), Expect = 1e-05
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
            A +KR++ V  L        L A F PFGD+  + +P    T        VEF     A
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 497 KAAFNSL 503
            AA +++
Sbjct: 68  AAAIDNM 74

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 88.4 bits (219), Expect = 4e-20
 Identities = 43/207 (20%), Positives = 78/207 (37%), Gaps = 29/207 (14%)

Query: 450 ILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTK 507
           +LV NL P R  P  L  LF  +GD+ RV +        LV+    NQA+ A + L   K
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65

Query: 508 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEE 567
               P+ +  +                  K++      E ++ +   ++     +   ++
Sbjct: 66  LHGKPIRITLS------------------KHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 107

Query: 568 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 627
              ++ +    P  TL++ N+  + +E+ ++  F   G +       +KD          
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR--------- 158

Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDE 654
               +Q  + E   QAL  L N  L E
Sbjct: 159 KMALIQMGSVEEAVQALIDLHNHDLGE 185

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 81.9 bits (202), Expect = 6e-18
 Identities = 32/208 (15%), Positives = 59/208 (28%), Gaps = 39/208 (18%)

Query: 580 DTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
           ++ L + NLN    T  S+   F   G +  V +   K               VQ     
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----------KENALVQMADGN 52

Query: 639 SLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK----------- 687
               A+  L    L    I +  S           +           S            
Sbjct: 53  QAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKN 112

Query: 688 ----------ILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFI 736
                     + + NIP    + +++ LF + G  +K  +  +K       R    ++  
Sbjct: 113 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMALIQMG 166

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWA 764
           +  EA +A+  L          L + ++
Sbjct: 167 SVEEAVQALIDLHNHDLGENHHLRVSFS 194

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 80.3 bits (198), Expect = 2e-17
 Identities = 43/197 (21%), Positives = 66/197 (33%), Gaps = 19/197 (9%)

Query: 336 SGRIFVRNLS-YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +  + V NL+   VT   L  LF  YG +  V +  +K     K  ALV       A  A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLA 57

Query: 395 YQHLDGTVFLGRMLHLIPGK----PKENEGNVDGKVHCCISERKLDAFNQVVEARSKR-- 448
             HL+G    G+ + +   K        EG  D  +        L  F +      +   
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 449 ----IILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGITGLVEFLQKNQAKAAFNS 502
                + + N+P      DLK LF   G +  G           L++     +A  A   
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 177

Query: 503 LAYTKFKE-VPLYLEWA 518
           L      E   L + ++
Sbjct: 178 LHNHDLGENHHLRVSFS 194

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 79.2 bits (195), Expect = 6e-17
 Identities = 39/183 (21%), Positives = 66/183 (36%), Gaps = 11/183 (6%)

Query: 225 HTIVVKNL-PAGVKKKDLKAYFKPL-PLASVRTTF--LGMAYIGFKDEKNCNKALNK-NK 279
             ++V NL P  V  + L   F     +  V+  F     A +   D      A++  N 
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 63

Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAK-HWKSQEDSVQFAEDIAESGR 338
               GK + I   SK  + +      ++   + +   +  H   +  S  F      S  
Sbjct: 64  HKLHGKPIRI-TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + + N+  +V+E+DL  LF   G     ++   K   K +  AL+     E A QA   L
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 178

Query: 399 DGT 401
              
Sbjct: 179 HNH 181

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 45.7 bits (108), Expect = 2e-05
 Identities = 20/127 (15%), Positives = 39/127 (30%), Gaps = 17/127 (13%)

Query: 28  KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           ++T + L   F   G V  V++ +  +      A +     +QAQ A+ + N   +    
Sbjct: 15  RVTPQSLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKP 70

Query: 88  IKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTF 147
           I++             + SK+       +   +    +D         K          F
Sbjct: 71  IRI-------------TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 148 SDFLQLH 154
                LH
Sbjct: 118 PPSATLH 124

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 85.9 bits (213), Expect = 4e-20
 Identities = 22/100 (22%), Positives = 43/100 (43%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
            Q+      +   E   +FV  +    TE+D+   F +YG +  + L +D+ T   KG+ 
Sbjct: 8   EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67

Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
           LV +   + A  A + L+G   +G+ + +     +     
Sbjct: 68  LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKG 107

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 72.0 bits (177), Expect = 3e-15
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G  + V  +  +A + ++ + F  +GE+K + L      +G  +G+  VE+ T  EA+ A
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 80

Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
           M+ L     L G+ + ++W   
Sbjct: 81  MEGL-NGQDLMGQPISVDWCFV 101

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 54.7 bits (132), Expect = 3e-09
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
                L++  ++  +TE+ I   F + G I ++ +    D ++ G     GY  V++ T 
Sbjct: 20  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL--DRRT-GY--LKGYTLVEYETY 74

Query: 638 ESLNQALKVLQNSSLDEHQI 657
           +    A++ L    L    I
Sbjct: 75  KEAQAAMEGLNGQDLMGQPI 94

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 50.8 bits (122), Expect = 7e-08
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
           + T+E +  KF E G + ++ L   + T  G  + +  + Y    +AQAA++  N   +
Sbjct: 32 EEATEEDIHDKFAEYGEIKNIHLNLDRRT--GYLKGYTLVEYETYKEAQAAMEGLNGQDL 89

Query: 84 FSSRIKVEKC 93
              I V+ C
Sbjct: 90 MGQPISVDWC 99

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 42.4 bits (100), Expect = 6e-05
 Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 8/77 (10%)

Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFN 501
           I+ V  +       D+   F  +G++  + +          G   LVE+    +A+AA  
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY-TLVEYETYKEAQAAME 82

Query: 502 SLAYTKFKEVPLYLEWA 518
            L        P+ ++W 
Sbjct: 83  GLNGQDLMGQPISVDWC 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 85.5 bits (212), Expect = 4e-20
 Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 8/96 (8%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFAL 382
           +D +++  IFV+ L   VT + +   F++ G +          + L  D+ET K KG A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 383 VTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           V+F  P  A  A    DG  F G  + +     + +
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 57.8 bits (140), Expect = 2e-10
 Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 7/89 (7%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP-----GQFLSMG 628
           E++   + T++++ L  N T +S+  +FK+ G I +     +           G+    G
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK--LKG 58

Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQI 657
              V F    S   A+          + I
Sbjct: 59  EATVSFDDPPSAKAAIDWFDGKEFSGNPI 87

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 54.7 bits (132), Expect = 3e-09
 Identities = 17/89 (19%), Positives = 29/89 (32%), Gaps = 10/89 (11%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFIT 737
           + I V+ +        V + FK  G +K         + L      +G  +G   V F  
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-TGKLKGEATVSFDD 66

Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
              AK A+          G  + + +A  
Sbjct: 67  PPSAKAAIDWF-DGKEFSGNPIKVSFATR 94

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 27 YKITQEQLKAKFEEKGTVT--------DVQLKYTTE-GKFRRFAFIGYHREDQAQAALDY 77
            +T E +   F++ G +          + L    E GK +  A + +     A+AA+D+
Sbjct: 17 ENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW 76

Query: 78 FNNTYVFSSRIKVEK 92
          F+      + IKV  
Sbjct: 77 FDGKEFSGNPIKVSF 91

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 84.8 bits (210), Expect = 6e-20
 Identities = 29/107 (27%), Positives = 50/107 (46%), Gaps = 8/107 (7%)

Query: 323 QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKET 374
              S    ++ +++  I+V+ L+ +VT DDL   F++ G +          + + +DKET
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 375 DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
            K KG A V++  P  A  A +  DG  F G  L +   + K    +
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 55.1 bits (133), Expect = 2e-09
 Identities = 14/105 (13%), Positives = 36/105 (34%), Gaps = 7/105 (6%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP-----GQF 624
              +  E   ++ +Y++ LN + T D +   FK+CG +       +           G+ 
Sbjct: 5   SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK- 63

Query: 625 LSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESE 669
              G   V +    +   A++          ++++  + +     
Sbjct: 64  -PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 54.0 bits (130), Expect = 5e-09
 Identities = 17/92 (18%), Positives = 32/92 (34%), Gaps = 8/92 (8%)

Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV---GSGLHRGFGFVE 734
               S I V+ +       ++ + FK  G +K       P   +     +G  +G   V 
Sbjct: 12  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           +     AK A++         G +L +  A +
Sbjct: 72  YEDPPTAKAAVEWF-DGKDFQGSKLKVSLARK 102

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 9/75 (12%)

Query: 27 YKITQEQLKAKFEEKGTVT--------DVQLKYTTE-GKFRRFAFIGYHREDQAQAALDY 77
            +T + L   F++ G V          + +    E GK +  A + Y     A+AA+++
Sbjct: 25 DSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW 84

Query: 78 FNNTYVFSSRIKVEK 92
          F+      S++KV  
Sbjct: 85 FDGKDFQGSKLKVSL 99

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 85.0 bits (211), Expect = 6e-20
 Identities = 25/83 (30%), Positives = 42/83 (50%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           +  ++++NLS  VTE DL  LF ++       +     T + +G A +TF   E A QA 
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 396 QHLDGTVFLGRMLHLIPGKPKEN 418
             ++G    G++L +  GK K+ 
Sbjct: 85  HLVNGYKLYGKILVIEFGKNKKQ 107

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 72.7 bits (179), Expect = 1e-15
 Identities = 25/103 (24%), Positives = 47/103 (45%), Gaps = 2/103 (1%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
           S+ +   E   +   SS    +    + ++N+  +  + ++  LF  F E K   +  +M
Sbjct: 2   SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM 61

Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
             +G  RG  F+ F  K  A +A+  +     LYG+ LV+E+ 
Sbjct: 62  -MTGRMRGQAFITFPNKEIAWQALHLV-NGYKLYGKILVIEFG 102

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 59.6 bits (145), Expect = 5e-11
 Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 5/95 (5%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
            EP+  LY+KNL+   TE  +   F +        +  +    +       G  F+ F  
Sbjct: 22  GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI--QFRMMTG---RMRGQAFITFPN 76

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEAT 671
           +E   QAL ++    L    + ++      +  + 
Sbjct: 77  KEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSG 111

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            ++T+  L + F          +++    G+ R  AFI +  ++ A  AL   N   ++ 
Sbjct: 35  PRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG 94

Query: 86  SRIKVE 91
             + +E
Sbjct: 95  KILVIE 100

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 45.0 bits (107), Expect = 7e-06
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL----- 487
           RK+  F+        +++ +KNL  R    DL +LF  F +     +    +TG      
Sbjct: 11  RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 70

Query: 488 -VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
            + F  K  A  A + +   K     L +E+ 
Sbjct: 71  FITFPNKEIAWQALHLVNGYKLYGKILVIEFG 102

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 83.7 bits (208), Expect = 8e-20
 Identities = 21/74 (28%), Positives = 39/74 (52%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
               ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 395 YQHLDGTVFLGRML 408
             +++ +   GR +
Sbjct: 66  IDNMNESELFGRTI 79

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 73.3 bits (181), Expect = 3e-16
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           T   + V  +  +     +   F  FG++  +++P     +  HRGF FVEF    +A  
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAAA 64

Query: 744 AMKALCQSTHLYGRRLVLEWAE 765
           A+  +   + L+GR + +  A+
Sbjct: 65  AIDNM-NESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 5/76 (6%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
                LY+  L     +  +   F   G I  + +    D ++  +    G+ FV+F   
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP--LDYET-EK--HRGFAFVEFELA 59

Query: 638 ESLNQALKVLQNSSLD 653
           E    A+  +  S L 
Sbjct: 60  EDAAAAIDNMNESELF 75

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 49.1 bits (118), Expect = 9e-08
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           ++  + L A F   G +TD+Q+    E  K R FAF+ +   + A AA+D  N + +F 
Sbjct: 17 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 76

Query: 86 SRIKVEK 92
            I+V  
Sbjct: 77 RTIRVNL 83

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 44.4 bits (106), Expect = 5e-06
 Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 6/66 (9%)

Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAK 497
           A +KR++ V  L        L A F PFGD+  + +P    T        VEF     A 
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 498 AAFNSL 503
           AA +++
Sbjct: 64  AAIDNM 69

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 84.3 bits (209), Expect = 1e-19
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 3/91 (3%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
            +  +++RNL Y +T +++  +F KYGP+ ++ +       +T+G A V +     A  A
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNA 63

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGK 425
             HL G     R L ++          +D K
Sbjct: 64  VDHLSGFNVSNRYLVVLYYNANRAFQKMDTK 94

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 71.2 bits (175), Expect = 4e-15
 Identities = 19/108 (17%), Positives = 45/108 (41%), Gaps = 13/108 (12%)

Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
           +    + +RN+P++    E+ ++F  +G ++ +R+      +   RG  +V +    +AK
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN----TPETRGTAYVVYEDIFDAK 61

Query: 743 RAMKALCQSTHLYGRRLVLEWAEEADNVEDIR--------KRTNRYFG 782
            A+  L    ++  R LV+ +       + +         K     +G
Sbjct: 62  NAVDHL-SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYG 108

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 65.5 bits (160), Expect = 3e-13
 Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 8/107 (7%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
           PE +  LYI+NL +  T + +   F K GPI  + V     P++       G  +V +  
Sbjct: 5   PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETR------GTAYVVYED 56

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQ 683
                 A+  L   ++    + +   N N   +    K+K   +   
Sbjct: 57  IFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 103

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 55.5 bits (134), Expect = 1e-09
 Identities = 22/107 (20%), Positives = 44/107 (41%), Gaps = 5/107 (4%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAFNSLA 504
           RI+ ++NLPY+    ++  +F  +G + ++ V     T     V +     AK A + L+
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68

Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEE--GEEGEEEK 549
                   L + +       +  +  K +E+ K  +E  G   +  K
Sbjct: 69  GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 115

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 49.7 bits (119), Expect = 1e-07
 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          YKIT E++   F + G +  +++  T   + R  A++ Y     A+ A+D+ +   V + 
Sbjct: 18 YKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNR 75

Query: 87 RIKVE 91
           + V 
Sbjct: 76 YLVVL 80

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 83.1 bits (206), Expect = 2e-19
 Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 8/88 (9%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFA 381
               +++  IFV+ L   VT + +   F++ G +          + L  D+ET K KG A
Sbjct: 7   HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 66

Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLH 409
            V+F  P  A  A    DG  F G  + 
Sbjct: 67  TVSFDDPPSAKAAIDWFDGKEFSGNPIK 94

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 56.2 bits (136), Expect = 4e-10
 Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 7/93 (7%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP-----GQF 624
                     + T++++ L  N T +S+  +FK+ G I +     +           G+ 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK- 61

Query: 625 LSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
              G   V F    S   A+          + I
Sbjct: 62  -LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 93

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 51.2 bits (123), Expect = 3e-08
 Identities = 17/97 (17%), Positives = 31/97 (31%), Gaps = 8/97 (8%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV---GSGLH 727
               + +    + I V+ +        V + FK  G +K       P   +     +G  
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 728 RGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
           +G   V F     AK A+          G  + + +A
Sbjct: 63  KGEATVSFDDPPSAKAAIDWF-DGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 27 YKITQEQLKAKFEEKGTVTD--------VQLKYTTE-GKFRRFAFIGYHREDQAQAALDY 77
            +T E +   F++ G +          + L    E GK +  A + +     A+AA+D+
Sbjct: 23 ENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW 82

Query: 78 FNNTYVFSSRIKVEK 92
          F+      + IKV  
Sbjct: 83 FDGKEFSGNPIKVSF 97

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 87.4 bits (216), Expect = 2e-19
 Identities = 41/212 (19%), Positives = 68/212 (32%), Gaps = 10/212 (4%)

Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNL-PAGVKKKDLKAYFKPL-PLASVRTTF--LGM 260
            P    +  ++   +       ++V NL P  V  + L   F     +  V+  F     
Sbjct: 15  VPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN 74

Query: 261 AYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKH 319
           A +   D      A++  N     GK + I      N        +D            H
Sbjct: 75  ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH 134

Query: 320 WKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG 379
              +  S  F      S  + + N+  +V+E+DL  LF   G     ++   K   K + 
Sbjct: 135 RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRK 190

Query: 380 FALVTFLMPEHATQAYQHLDGT-VFLGRMLHL 410
            AL+     E A QA   L    +     L +
Sbjct: 191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 87.0 bits (215), Expect = 2e-19
 Identities = 46/209 (22%), Positives = 79/209 (37%), Gaps = 29/209 (13%)

Query: 448 RIILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 505
            ++LV NL P R  P  L  LF  +GD+ RV +        LV+    NQA+ A + L  
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 94

Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
            K    P+ +  +               +  +   EG+E +   K+      ++   P  
Sbjct: 95  HKLHGKPIRITLSK-------------HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGS 141

Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
           +     + +    P  TL++ N+  + +E+ ++  F   G +       +KD        
Sbjct: 142 K-----NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR------- 189

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE 654
                 +Q  + E   QAL  L N  L E
Sbjct: 190 --KMALIQMGSVEEAVQALIDLHNHDLGE 216

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 83.5 bits (206), Expect = 3e-18
 Identities = 32/212 (15%), Positives = 59/212 (27%), Gaps = 39/212 (18%)

Query: 576 EPEPDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
               ++ L + NLN    T  S+   F   G +  V +   K               VQ 
Sbjct: 30  AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK----------ENALVQM 79

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK------- 687
                   A+  L    L    I +  S           +           S        
Sbjct: 80  ADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 139

Query: 688 --------------ILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGF 732
                         + + NIP    + +++ LF + G  +K  +  +K       R    
Sbjct: 140 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMAL 193

Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
           ++  +  EA +A+  L          L + ++
Sbjct: 194 IQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 80.0 bits (197), Expect = 5e-17
 Identities = 45/199 (22%), Positives = 66/199 (33%), Gaps = 19/199 (9%)

Query: 334 AESGRIFVRNLS-YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           A +  + V NL+   VT   L  LF  YG +  V     K     K  ALV       A 
Sbjct: 32  AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQ 86

Query: 393 QAYQHLDGTVFLGRMLHLIPGK----PKENEGNVDGKVHCCISERKLDAFNQVVEARSKR 448
            A  HL+G    G+ + +   K        EG  D  +        L  F +      + 
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146

Query: 449 I------ILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGITGLVEFLQKNQAKAAF 500
           I      + + N+P      DLK LF   G +  G           L++     +A  A 
Sbjct: 147 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 206

Query: 501 NSLAYTKFKE-VPLYLEWA 518
             L      E   L + ++
Sbjct: 207 IDLHNHDLGENHHLRVSFS 225

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 41.5 bits (97), Expect = 5e-04
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 4/77 (5%)

Query: 28  KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           ++T + L   F   G V  V++ +  +      A +     +QAQ A+ + N   +    
Sbjct: 46  RVTPQSLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKP 101

Query: 88  IKVEKCSNLGDTTKPKS 104
           I++    +       + 
Sbjct: 102 IRITLSKHQNVQLPREG 118

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 85.5 bits (211), Expect = 4e-19
 Identities = 26/194 (13%), Positives = 61/194 (31%), Gaps = 35/194 (18%)

Query: 579 PDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
               L +  L+      D +   F   G +  V   + K           G   V+    
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP----------GAAMVEMADG 52

Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEA-----------------------TTVK 674
            ++++A+  L N+ +   ++ +  S +                             +T +
Sbjct: 53  YAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPE 112

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
           + + N  +   + +   N P +  +    E+    G  +   + K   G       G +E
Sbjct: 113 QAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV-KVFSGKSERSSSGLLE 171

Query: 735 FITKNEAKRAMKAL 748
           + +K++A   +  L
Sbjct: 172 WDSKSDALETLGFL 185

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 84.0 bits (207), Expect = 1e-18
 Identities = 24/209 (11%), Positives = 60/209 (28%), Gaps = 23/209 (11%)

Query: 448 RIILVKNLPYRTL-PTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 505
            +++V  L    +    +  +F  +G++ +V          +VE         A   L  
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNN 64

Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
                  + +  +                K+     G+    E    + ++ ++      
Sbjct: 65  NFMFGQKMNVCVS----------------KQPAIMPGQSYGLEDGSCSYKDFSESRNNRF 108

Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
               +  + R   P   L+  N     TE++      + G     +V  K          
Sbjct: 109 STPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV--KVFSGKSE--- 163

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE 654
               G +++ ++    + L  L +  +  
Sbjct: 164 RSSSGLLEWDSKSDALETLGFLNHYQMKN 192

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 79.7 bits (196), Expect = 4e-17
 Identities = 35/196 (17%), Positives = 64/196 (32%), Gaps = 24/196 (12%)

Query: 334 AESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           A+S  + V  L    +  D +  +F  YG + +V     K      G A+V         
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVD 56

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCC------ISERKLDAFNQVVEARS 446
           +A  HL+     G+ +++   K           +          SE + + F+   +A  
Sbjct: 57  RAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAK 116

Query: 447 KRI------ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKN 494
            RI      +   N P      +   + +  G      V  +         GL+E+  K+
Sbjct: 117 NRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176

Query: 495 QAKAAFNSLAYTKFKE 510
            A      L + + K 
Sbjct: 177 DALETLGFLNHYQMKN 192

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 79.7 bits (196), Expect = 4e-17
 Identities = 25/188 (13%), Positives = 58/188 (30%), Gaps = 7/188 (3%)

Query: 226 TIVVKNL-PAGVKKKDLKAYFKPL-PLASVRTTF--LGMAYIGFKDEKNCNKA---LNKN 278
            ++V  L  + +    +   F     +  V+      G A +   D    ++A   LN N
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65

Query: 279 KSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGR 338
             F +   + + K       +  G  D + +    +    +  S  +          S  
Sbjct: 66  FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV 125

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +   N    VTE++  ++ ++ G      + +     +     L+ +     A +    L
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185

Query: 399 DGTVFLGR 406
           +       
Sbjct: 186 NHYQMKNP 193

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 44.3 bits (104), Expect = 4e-05
 Identities = 8/64 (12%), Positives = 23/64 (35%), Gaps = 1/64 (1%)

Query: 29  ITQEQLKAKFEEKGTVTDVQLK-YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           +T+E      +E G      +K ++ + +      + +  +  A   L + N+  + +  
Sbjct: 135 VTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPN 194

Query: 88  IKVE 91
               
Sbjct: 195 GPYP 198

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 41.6 bits (97), Expect = 3e-04
 Identities = 18/117 (15%), Positives = 36/117 (30%), Gaps = 6/117 (5%)

Query: 28  KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           K+  +++   F   G V  V+   +  G     A +          A+ + NN ++F  +
Sbjct: 16  KMNCDRVFNVFCLYGNVEKVKFMKSKPG----AAMVEMADGYAVDRAITHLNNNFMFGQK 71

Query: 88  IKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKND 144
           + V           P         S +Y+        +   PE    ++    S   
Sbjct: 72  MNVCVSKQ--PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVL 126

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 82.3 bits (204), Expect = 4e-19
 Identities = 27/84 (32%), Positives = 42/84 (50%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
               +FV N+ Y  TE+ L  +F + GP+    L  D+ET K KG+    +   E A  A
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 395 YQHLDGTVFLGRMLHLIPGKPKEN 418
            ++L+G  F GR L +     ++N
Sbjct: 67  MRNLNGREFSGRALRVDNAASEKN 90

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 64.6 bits (158), Expect = 6e-13
 Identities = 24/98 (24%), Positives = 47/98 (47%), Gaps = 2/98 (2%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
             ++   + V NIP++A + +++++F   G +   RL      +G  +G+GF E+  +  
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQET 62

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTN 778
           A  AM+ L       GR L ++ A    N E+++    
Sbjct: 63  ALSAMRNL-NGREFSGRALRVDNAASEKNKEELKSLGT 99

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 11/84 (13%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD---PKSPGQFLSMGY 629
           +        ++++ N+ + +TE+ ++  F + GP+ S  +   ++   PK        GY
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPK--------GY 52

Query: 630 GFVQFYTRESLNQALKVLQNSSLD 653
           GF ++  +E+   A++ L      
Sbjct: 53  GFCEYQDQETALSAMRNLNGREFS 76

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           Y+ T+EQLK  F E G V   +L Y  E GK + + F  Y  ++ A +A+   N      
Sbjct: 18  YEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG 77

Query: 86  SRIKVEKCSNLGDTTKPKSWSKYAP 110
             ++V+  ++  +  + KS    AP
Sbjct: 78  RALRVDNAASEKNKEELKSLGTGAP 102

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 81.9 bits (203), Expect = 4e-19
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 4/88 (4%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
            ES  + + NLSY+ TE+ L ++FEK       I     +  K+KG+A + F   E A +
Sbjct: 13  GESKTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFIEFASFEDAKE 68

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
           A    +     GR + L    P+ +  +
Sbjct: 69  ALNSCNKREIEGRAIRLELQGPRGSPNS 96

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 64.6 bits (158), Expect = 6e-13
 Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 7/92 (7%)

Query: 676 KSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
            S N      SK L + N+ + A +  ++E+F+       +++P+    +G  +G+ F+E
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF---IKVPQNQ--NGKSKGYAFIE 59

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           F +  +AK A+ +      + GR + LE    
Sbjct: 60  FASFEDAKEALNSC-NKREIEGRAIRLELQGP 90

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
                       TL + NL++++TE++++  F+K      + V + ++ KS       GY
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF---IKVPQNQNGKSK------GY 55

Query: 630 GFVQFYTRESLNQALKVLQNSSLD 653
            F++F + E   +AL       ++
Sbjct: 56  AFIEFASFEDAKEALNSCNKREIE 79

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          Y  T+E L+  FE+   +  V       GK + +AFI +   + A+ AL+  N   +   
Sbjct: 25 YSATEETLQEVFEKATFI-KVPQNQN--GKSKGYAFIEFASFEDAKEALNSCNKREIEGR 81

Query: 87 RIKVEK 92
           I++E 
Sbjct: 82 AIRLEL 87

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 81.2 bits (201), Expect = 8e-19
 Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           +   R+ V N+ +   + DL ++F ++G + +V +  ++    +KGF  VTF     A +
Sbjct: 13  STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADR 70

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
           A + L GTV  GR + +     +  
Sbjct: 71  AREKLHGTVVEGRKIEVNNATARVM 95

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.9 bits (177), Expect = 2e-15
 Identities = 27/90 (30%), Positives = 48/90 (53%), Gaps = 4/90 (4%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
            ++ +K T  ++ V NIPF+ +  ++ ++F  FG++  V +     GS   +GFGFV F 
Sbjct: 7   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFE 63

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
              +A RA + L   T + GR++ +  A  
Sbjct: 64  NSADADRAREKL-HGTVVEGRKIEVNNATA 92

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 58.5 bits (142), Expect = 8e-11
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
                      L++ N+ F   +  +R+ F + G I  V +   +         S G+GF
Sbjct: 7   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-------SKGFGF 59

Query: 632 VQFYTRESLNQALKVLQNSSLD 653
           V F      ++A + L  + ++
Sbjct: 60  VTFENSADADRAREKLHGTVVE 81

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          ++     L+  F + G + DV++ +   G  + F F+ +     A  A +  + T V   
Sbjct: 25 FRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEGR 83

Query: 87 RIKVEK 92
          +I+V  
Sbjct: 84 KIEVNN 89

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 12/62 (19%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFN 501
           + V N+P+R    DL+ +F  FG +  V +    I         G V F     A  A  
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKGFGFVTFENSADADRARE 73

Query: 502 SL 503
            L
Sbjct: 74  KL 75

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 81.3 bits (201), Expect = 1e-18
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 1/95 (1%)

Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
           +      E +    ++ V NL + V++ D+ +LF ++G L +  +  D  + ++ G A V
Sbjct: 23  DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADV 81

Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            F     A +A +   G    GR + +     + +
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 116

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 67.0 bits (164), Expect = 2e-13
 Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 3/92 (3%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
                   +TG+K+LV N+ F    ++++ELF  FG LK   +      SG   G   V 
Sbjct: 25  GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR--SGRSLGTADVH 82

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           F  + +A +AMK   +   L GR + ++    
Sbjct: 83  FERRADALKAMKQY-KGVPLDGRPMDIQLVAS 113

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 63.2 bits (154), Expect = 3e-12
 Identities = 20/98 (20%), Positives = 39/98 (39%), Gaps = 6/98 (6%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
                E    L + NL+F  ++  I+  F + G +    V   +     G+  S+G   V
Sbjct: 28  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS----GR--SLGTADV 81

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA 670
            F  R    +A+K  +   LD   ++++     ++ E 
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 119

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 53.1 bits (128), Expect = 9e-09
 Identities = 10/65 (15%), Positives = 26/65 (40%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           + ++   ++  F E GT+    + Y   G+    A + + R   A  A+  +    +   
Sbjct: 45  FGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR 104

Query: 87  RIKVE 91
            + ++
Sbjct: 105 PMDIQ 109

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 42.4 bits (100), Expect = 6e-05
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 504
           +LV NL +     D++ LF  FG L +  V     G    T  V F ++  A  A     
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97

Query: 505 YTKFKEVPLYLEWAPE 520
                  P+ ++    
Sbjct: 98  GVPLDGRPMDIQLVAS 113

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 80.8 bits (200), Expect = 1e-18
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
             G++F+  L+    E  L  +F K+GP++EV+L  D+ T K++GFA +TF  P  A  A
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64

Query: 395 YQHLDGTVFLGRML 408
            + ++G    G+ +
Sbjct: 65  AKDMNGKSLHGKAI 78

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 68.1 bits (167), Expect = 4e-14
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 6/89 (6%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           E +    L+I  LN  + E  ++  F K GPI+ V + + +  KS       G+ F+ F 
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR------GFAFITFE 56

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNR 664
                  A K +   SL    I+++++ +
Sbjct: 57  NPADAKNAAKDMNGKSLHGKAIKVEQAKK 85

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 63.1 bits (154), Expect = 3e-12
 Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 3/101 (2%)

Query: 680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 739
           V      K+ +  +  +  +  ++ +F   G +  V L K    +   RGF F+ F    
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR--TSKSRGFAFITFENPA 59

Query: 740 EAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
           +AK A K +     L+G+ + +E A++       R+R    
Sbjct: 60  DAKNAAKDM-NGKSLHGKAIKVEQAKKPSFQSGGRRRPPAS 99

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 48.9 bits (117), Expect = 3e-07
 Identities = 20/66 (30%), Positives = 31/66 (46%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           +  ++ LKA F + G +++V L      K R FAFI +     A+ A    N   +   
Sbjct: 17 RETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGK 76

Query: 87 RIKVEK 92
           IKVE+
Sbjct: 77 AIKVEQ 82

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 80.0 bits (198), Expect = 1e-18
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S ++ V N+S T T  +L   FE+YGP+ E  +         K +A V     E A +A 
Sbjct: 10  STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAI 61

Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGN 421
           + LD T F G+ +H+     +    +
Sbjct: 62  RGLDNTEFQGKRMHVQLSTSRLRTAS 87

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 70.7 bits (174), Expect = 3e-15
 Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 10/90 (11%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
           SS  + +  +K+ V NI       E+   F+ +G +    +          + + FV   
Sbjct: 2   SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---------KDYAFVHME 52

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
              +A  A++ L  +T   G+R+ ++ +  
Sbjct: 53  RAEDAVEAIRGL-DNTEFQGKRMHVQLSTS 81

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 13/77 (16%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
            +  T L++ N++   T   +R  F++ GP+    + +              Y FV    
Sbjct: 7   GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------------DYAFVHMER 53

Query: 637 RESLNQALKVLQNSSLD 653
            E   +A++ L N+   
Sbjct: 54  AEDAVEAIRGLDNTEFQ 70

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 7/65 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             T ++L+AKFEE G V +  +        + +AF+   R + A  A+   +NT     
Sbjct: 20 PTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQGK 72

Query: 87 RIKVE 91
          R+ V+
Sbjct: 73 RMHVQ 77

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSL 503
           ++   + V N+       +L+A FE +G +    +V  Y     V   +   A  A   L
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY---AFVHMERAEDAVEAIRGL 64

Query: 504 AYTKFKEVPLYLEWA 518
             T+F+   ++++ +
Sbjct: 65  DNTEFQGKRMHVQLS 79

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 79.8 bits (198), Expect = 2e-18
 Identities = 18/83 (21%), Positives = 36/83 (43%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           +  +FV +L+  V ++ L   F+ +       +  D +T  ++G+  V+F   + A  A 
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 396 QHLDGTVFLGRMLHLIPGKPKEN 418
             + G    GR L +      E+
Sbjct: 61  DSMQGQDLNGRPLRINWAAKLEH 83

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 60.6 bits (148), Expect = 9e-12
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V ++        +   FK F       +   M  +G  RG+GFV F ++++A+ AM 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
           ++ Q   L GR L + WA + ++
Sbjct: 62  SM-QGQDLNGRPLRINWAAKLEH 83

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 53.7 bits (130), Expect = 2e-09
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L++ +LN N  ++++R  FK      S  V    D ++ G   S GYGFV F +++    
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW--DMQT-GS--SRGYGFVSFTSQDDAQN 58

Query: 643 ALKVLQNSSLDEHQI 657
           A+  +Q   L+   +
Sbjct: 59  AMDSMQGQDLNGRPL 73

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 11/65 (16%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            +  E L+  F++  +     + +  + G  R + F+ +  +D AQ A+D      +  
Sbjct: 11 VNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG 70

Query: 86 SRIKV 90
            +++
Sbjct: 71 RPLRI 75

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 80.4 bits (199), Expect = 2e-18
 Identities = 21/87 (24%), Positives = 39/87 (44%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +   ++V  L   V+E  L +LF + GP+    +P D+ T + +G+  V FL  E A  A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
            + +D     G+ + +          +
Sbjct: 74  IKIMDMIKLYGKPIRVNKASAHNKNLS 100

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 72.3 bits (178), Expect = 1e-15
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + V  +  +  +  + ELF   G +    +PK  V +G H+G+GFVEF+++ +A  A+
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-TGQHQGYGFVEFLSEEDADYAI 74

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
           K +     LYG+ + +  A  
Sbjct: 75  KIM-DMIKLYGKPIRVNKASA 94

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 59.6 bits (145), Expect = 4e-11
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
            E   D T+Y+  L+   +E  +   F + GP+ +  + + +           GYGFV+F
Sbjct: 10  SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQ-----HQGYGFVEF 64

Query: 635 YTRESLNQALKVLQNSSLD 653
            + E  + A+K++    L 
Sbjct: 65  LSEEDADYAIKIMDMIKLY 83

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 50.0 bits (120), Expect = 9e-08
 Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 6  SGPVVPRNHISLL---DLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFA 61
          SGP+  RN  + +    LD      K+++  L   F + G V +  +      G+ + + 
Sbjct: 6  SGPISERNQDATVYVGGLD-----EKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 62 FIGYHREDQAQAALDYFNNTYVFSSRIKVEK 92
          F+ +  E+ A  A+   +   ++   I+V K
Sbjct: 61 FVEFLSEEDADYAIKIMDMIKLYGKPIRVNK 91

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 6/88 (6%)

Query: 437 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEF 490
           +   + E      + V  L  +     L  LF   G +    +P   +TG       VEF
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 491 LQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
           L +  A  A   +   K    P+ +  A
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKA 92

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 79.6 bits (197), Expect = 4e-18
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
            S  +FV+ LS   TE+ L + F+         +  D+ET  +KGF  V F   E A  A
Sbjct: 14  PSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAA 70

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
            + ++     G  + L   KPK   G+
Sbjct: 71  KEAMEDGEIDGNKVTLDWAKPKGEGGS 97

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 22/92 (23%), Positives = 43/92 (46%), Gaps = 5/92 (5%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
               N   Q    + V+ +     +   E L ++F      R+      +G  +GFGFV+
Sbjct: 5   SSGPNARSQPSKTLFVKGLSEDTTE---ETLKESFDGSVRARIVTDRE-TGSSKGFGFVD 60

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           F ++ +AK A +A+ +   + G ++ L+WA+ 
Sbjct: 61  FNSEEDAKAAKEAM-EDGEIDGNKVTLDWAKP 91

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 55.7 bits (135), Expect = 7e-10
 Identities = 19/88 (21%), Positives = 42/88 (47%), Gaps = 8/88 (9%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
                   +P  TL++K L+ ++TE++++  F          +    D ++ G   S G+
Sbjct: 5   SSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIV--TDRET-GS--SKGF 56

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQI 657
           GFV F + E    A + +++  +D +++
Sbjct: 57  GFVDFNSEEDAKAAKEAMEDGEIDGNKV 84

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 13/67 (19%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
             T+E LK  F+        ++    E G  + F F+ ++ E+ A+AA +   +  +  
Sbjct: 25 EDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG 81

Query: 86 SRIKVEK 92
          +++ ++ 
Sbjct: 82 NKVTLDW 88

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 79.7 bits (197), Expect = 4e-18
 Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 1/98 (1%)

Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
             +E     + +  ++  +F   L+  +   DL   F   G + +V +  D+ + ++KG 
Sbjct: 10  PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69

Query: 381 ALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           A V F   +    A   L G   LG  + +   + ++N
Sbjct: 70  AYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKN 106

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 68.1 bits (167), Expect = 5e-14
 Identities = 16/118 (13%), Positives = 34/118 (28%), Gaps = 12/118 (10%)

Query: 558 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 617
           +            ++   E     T++   L        +   F   G +  V +   ++
Sbjct: 3   SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62

Query: 618 ---PKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT 672
               K        G  +V+F   +S+  A+  L    L    I ++ S       +  
Sbjct: 63  SRRSK--------GIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLSGP 111

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.9 bits (138), Expect = 4e-10
 Identities = 16/108 (14%), Positives = 42/108 (38%), Gaps = 3/108 (2%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
           S+ +           + +  ++    +    +  + +  ++E+ F A G+++ VR+    
Sbjct: 2   SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61

Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
             S   +G  +VEF        A+        L G  ++++ ++   N
Sbjct: 62  N-SRRSKGIAYVEFCEIQSVPLAIG--LTGQRLLGVPIIVQASQAEKN 106

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 8/97 (8%)

Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASV-----R 254
           S  ++   P   PV      +R   T+    L A ++ +DL+ +F  +  +  V     R
Sbjct: 2   SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61

Query: 255 TT--FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
            +    G+AY+ F + ++   A+        G  + +
Sbjct: 62  NSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIV 98

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.9 bits (99), Expect = 7e-05
 Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 2/67 (2%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            +I    L+  F   G V DV++       + +  A++ +        A+       +  
Sbjct: 35  ARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLG 93

Query: 86  SRIKVEK 92
             I V+ 
Sbjct: 94  VPIIVQA 100

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 78.5 bits (194), Expect = 8e-18
 Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
               RI+V NL   +   D+  +F KYG + ++ L   +       FA V F  P  A  
Sbjct: 20  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAED 76

Query: 394 AYQHLDGTVFLGRML 408
           A    DG  + G  L
Sbjct: 77  AVYGRDGYDYDGYRL 91

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 72.0 bits (177), Expect = 2e-15
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
              +I V N+P   +  ++E++F  +G ++ + L  +  G      F FVEF    +A+ 
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG----PPFAFVEFEDPRDAED 76

Query: 744 AMKALCQSTHLYGRRLVLEWAEE 766
           A+          G RL +E+   
Sbjct: 77  AVYGR-DGYDYDGYRLRVEFPRS 98

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.3 bits (157), Expect = 1e-12
 Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 10/93 (10%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                D  +Y+ NL  +     I   F K G I  + +  ++            + FV+F
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP--------PFAFVEF 68

Query: 635 YTRESLNQALKVLQNSSLDEHQI--ELKRSNRN 665
                   A+        D +++  E  RS R 
Sbjct: 69  EDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 101

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            I  + ++  F + G + D+ LK    G    FAF+ +     A+ A+   +       
Sbjct: 32 PDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAVYGRDGYDYDGY 89

Query: 87 RIKVE 91
          R++VE
Sbjct: 90 RLRVE 94

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 18/84 (21%), Positives = 31/84 (36%), Gaps = 9/84 (10%)

Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLV------PPYGITGLVEFLQKNQAK 497
             +   I V NLP      D++ +F  +G +  + +      PP+     VEF     A+
Sbjct: 19  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAF---VEFEDPRDAE 75

Query: 498 AAFNSLAYTKFKEVPLYLEWAPEG 521
            A        +    L +E+   G
Sbjct: 76  DAVYGRDGYDYDGYRLRVEFPRSG 99

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 78.1 bits (193), Expect = 8e-18
 Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 7/90 (7%)

Query: 331 EDIAESGR-IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           ED   S + ++VRNL  + +E+ + K F    P A           K + +A V F   E
Sbjct: 9   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE------RVKKIRDYAFVHFSNRE 62

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            A +A + L+G V  G  + +   KP + +
Sbjct: 63  DAVEAMKALNGKVLDGSPIEVTLAKPVDKD 92

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 71.5 bits (176), Expect = 2e-15
 Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 11/90 (12%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
              +E        LY++NL  +++E+ I + F    P A   V + +            Y
Sbjct: 5   SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR-----------DY 53

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIEL 659
            FV F  RE   +A+K L    LD   IE+
Sbjct: 54  AFVHFSNREDAVEAMKALNGKVLDGSPIEV 83

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 65.4 bits (160), Expect = 3e-13
 Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            KIL VRN+     +  +E+ F         R+ K        R + FV F  + +A  A
Sbjct: 15  VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVEA 67

Query: 745 MKALCQSTHLYGRRLVLEWAEEADN 769
           MKAL     L G  + +  A+  D 
Sbjct: 68  MKAL-NGKVLDGSPIEVTLAKPVDK 91

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 50.7 bits (122), Expect = 5e-08
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             ++E ++ +F         ++K     K R +AF+ +   + A  A+   N   +  S
Sbjct: 25 LSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKALNGKVLDGS 79

Query: 87 RIKVE 91
           I+V 
Sbjct: 80 PIEVT 84

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 15/73 (20%), Positives = 24/73 (32%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY 505
           S +I+ V+NL   T    ++  F          V        V F  +  A  A  +L  
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 73

Query: 506 TKFKEVPLYLEWA 518
                 P+ +  A
Sbjct: 74  KVLDGSPIEVTLA 86

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 78.5 bits (194), Expect = 8e-18
 Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 3/96 (3%)

Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
           ED V+   +      +F+ NL+   +  +L     +     ++ + +D  T   + F  V
Sbjct: 6   EDPVE-GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYV 63

Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            F   E   +A + L G    G  + L   K ++  
Sbjct: 64  DFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDGT 98

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 70.0 bits (172), Expect = 7e-15
 Identities = 19/94 (20%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
           +  E  E      L+I NLN N +   ++    +      + V   +         +  +
Sbjct: 7   DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT------NRKF 60

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
           G+V F + E L +AL+ L    +  ++I+L++  
Sbjct: 61  GYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK 93

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + + N+      +E++           + +     G+   R FG+V+F +  + ++A++
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN--RKFGYVDFESAEDLEKALE 76

Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
                  ++G  + LE  +  D 
Sbjct: 77  L--TGLKVFGNEIKLEKPKGRDG 97

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             +  +LK    E     D+ +     G  R+F ++ +   +  + AL+      VF +
Sbjct: 27 PNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN 85

Query: 87 RIKVEK 92
           IK+EK
Sbjct: 86 EIKLEK 91

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 78.0 bits (193), Expect = 9e-18
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            I+V NL Y+ T + + +LF ++G +  V L  D+ET K KGF  V     E  ++A   
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAK 61

Query: 398 LDGTVFLGRMLHLIPGKPKEN 418
           LD T F+GR + +    PK++
Sbjct: 62  LDNTDFMGRTIRVTEANPKKS 82

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 60.6 bits (148), Expect = 9e-12
 Identities = 24/94 (25%), Positives = 42/94 (44%), Gaps = 6/94 (6%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            I V N+ + A   +V+ELF  FG++  V+L      +   +GFGFVE   +     A+ 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVEM-QEESVSEAIA 60

Query: 747 ALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
            L  +T   GR + +  A      + +    + +
Sbjct: 61  KL-DNTDFMGRTIRVTEANPK---KSLEHHHHHH 90

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 6/67 (8%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
          Y  T EQ+K  F + G V +V+L   + T   K + F F+   +E+    A+   +NT  
Sbjct: 11 YSATSEQVKELFSQFGKVFNVKLIYDRET--KKPKGFGFVEM-QEESVSEAIAKLDNTDF 67

Query: 84 FSSRIKV 90
              I+V
Sbjct: 68 MGRTIRV 74

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 41.4 bits (98), Expect = 6e-05
 Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            +Y+ NL +++T + ++  F + G + +V +   ++     +    G+GFV+    ES++
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRE---TKK--PKGFGFVEMQE-ESVS 56

Query: 642 QALKVLQNSSLDEHQI 657
           +A+  L N+      I
Sbjct: 57  EAIAKLDNTDFMGRTI 72

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 78.5 bits (194), Expect = 9e-18
 Identities = 23/88 (26%), Positives = 40/88 (45%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           +D +    +FV +LS  +T +D+   F  +G +++  +  D  T K+KG+  V+F     
Sbjct: 10  KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           A  A Q + G    GR +       K  
Sbjct: 70  AENAIQQMGGQWLGGRQIRTNWATRKPP 97

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 59.7 bits (145), Expect = 4e-11
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V ++  +    +++  F  FG +   R+ K M  +G  +G+GFV F  K +A+ A++
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAENAIQ 75

Query: 747 ALCQSTHLYGRRLVLEWAEE 766
            +     L GR++   WA  
Sbjct: 76  QM-GGQWLGGRQIRTNWATR 94

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 58.9 bits (143), Expect = 7e-11
 Identities = 23/113 (20%), Positives = 49/113 (43%), Gaps = 5/113 (4%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           ++++      +++ +L+   T + I+  F   G I+   V +  D  + G+  S GYGFV
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVK--DMAT-GK--SKGYGFV 62

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
            F+ +     A++ +    L   QI    + R   +  +T +  +      +G
Sbjct: 63  SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           +IT E +KA F   G ++D ++      GK + + F+ +  +  A+ A+      ++  
Sbjct: 25 PEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG 84

Query: 86 SRIKV 90
           +I+ 
Sbjct: 85 RQIRT 89

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 77.7 bits (192), Expect = 1e-17
 Identities = 20/83 (24%), Positives = 33/83 (39%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
               I V+N+ +TV+ D++   F  Y  +   +     E     G A+V F   + AT A
Sbjct: 14  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 395 YQHLDGTVFLGRMLHLIPGKPKE 417
              L+      R + L+ G    
Sbjct: 74  VIDLNDRPIGSRKVKLVLGSGPS 96

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 67.7 bits (166), Expect = 4e-14
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEF 735
            ++  K   + I V+N+PF     E+ + F  +  +   V L       G+  G   V F
Sbjct: 7   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE--KGMPTGEAMVAF 64

Query: 736 ITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
            +++EA  A+  L     +  R++ L   
Sbjct: 65  ESRDEATAAVIDL-NDRPIGSRKVKLVLG 92

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 63.1 bits (154), Expect = 2e-12
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
               T + ++N+ F  + D I   F     I   +V  K + K  G     G   V F +
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPG-SVCLKYNEK--GM--PTGEAMVAFES 66

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSN 663
           R+    A+  L +  +   +++L   +
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVKLVLGS 93

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          + ++ +++   F     +   V LKY  +G     A + +   D+A AA+   N+  + S
Sbjct: 25 FTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS 84

Query: 86 SRIKVEKCS 94
           ++K+   S
Sbjct: 85 RKVKLVLGS 93

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 13/83 (15%), Positives = 27/83 (32%), Gaps = 9/83 (10%)

Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALN 276
             I V+N+P  V   ++  +F    +                G A + F+       A+ 
Sbjct: 16  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 277 K-NKSFWKGKQLNIYKYSKDNSA 298
             N      +++ +   S  +S 
Sbjct: 76  DLNDRPIGSRKVKLVLGSGPSSG 98

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 6/64 (9%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 499
              II V+N+P+     ++   F  +  +   +   Y   G      +V F  +++A AA
Sbjct: 14  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 500 FNSL 503
              L
Sbjct: 74  VIDL 77

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 78.1 bits (193), Expect = 1e-17
 Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 1/87 (1%)

Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
           +        +   G++ V NL + V++ D+ +LF ++G L +  +  D  + ++ G A V
Sbjct: 17  DSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADV 75

Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHL 410
            F     A +A +  +G    GR +++
Sbjct: 76  HFERKADALKAMKQYNGVPLDGRPMNI 102

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 65.8 bits (161), Expect = 3e-13
 Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
                   +TG K+LV N+ F    ++++ELF  FG LK   +      SG   G   V 
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR--SGRSLGTADVH 76

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
           F  K +A +AMK       L GR + ++   
Sbjct: 77  FERKADALKAMKQY-NGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 62.3 bits (152), Expect = 4e-12
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
                E    L + NL+F  ++  I+  F + G +    V   +     G+  S+G   V
Sbjct: 22  GGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS----GR--SLGTADV 75

Query: 633 QFYTRESLNQALKVLQNSSLD 653
            F  +    +A+K      LD
Sbjct: 76  HFERKADALKAMKQYNGVPLD 96

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 11/65 (16%), Positives = 28/65 (43%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           + ++   ++  F E GT+    + Y   G+    A + + R+  A  A+  +N   +   
Sbjct: 39  FGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 98

Query: 87  RIKVE 91
            + ++
Sbjct: 99  PMNIQ 103

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 41.5 bits (98), Expect = 9e-05
 Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 5/59 (8%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 503
           +LV NL +     D++ LF  FG L +  V     G    T  V F +K  A  A    
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 77.2 bits (191), Expect = 1e-17
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGP--LAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
            +++ NL++  T++DLT+     G   + E+    ++   ++KGFALV       + +  
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
             L      G+   + P    E
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLE 84

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 13/82 (15%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            + + N+ +     ++ E   + G  ++  ++  +    +G  +GF  V   ++  +K+ 
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKKL 61

Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
           M  L     L+G+  V+  + +
Sbjct: 62  MDLL-PKRELHGQNPVVTPSNK 82

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGP--IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           LYI NL + +T++ +       G   I  +     +     GQ  S G+  V   +  S 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA---NGQ--SKGFALVGVGSEASS 58

Query: 641 NQALKVLQNSSLDEHQI 657
            + + +L    L     
Sbjct: 59  KKLMDLLPKRELHGQNP 75

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 27 YKITQEQLKAKFEEKGT--VTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
          +  T E L       G   + +++    +    G+ + FA +G   E  ++  +D     
Sbjct: 11 WWTTDEDLTEAVHSLGVNDILEIKFFENRAN--GQSKGFALVGVGSEASSKKLMDLLPKR 68

Query: 82 YVFSSRIKVEKCS 94
           +      V   +
Sbjct: 69 ELHGQNPVVTPSN 81

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 77.7 bits (192), Expect = 2e-17
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 2/78 (2%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           E+ ++  R+ V N+ +   + DL ++F ++G + +V +  ++    +KGF  VTF     
Sbjct: 24  ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSAD 81

Query: 391 ATQAYQHLDGTVFLGRML 408
           A +A + L GTV  GR +
Sbjct: 82  ADRAREKLHGTVVEGRKI 99

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.6 bits (158), Expect = 6e-13
 Identities = 30/108 (27%), Positives = 51/108 (47%), Gaps = 6/108 (5%)

Query: 661 RSNRNLESEATTVKRKSS--NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP 718
            S+ +    +  V R S      K    ++ V NIPF+ +  ++ ++F  FG++  V + 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62

Query: 719 KKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
               GS   +GFGFV F    +A RA + L   T + GR++ +  A  
Sbjct: 63  FNERGS---KGFGFVTFENSADADRAREKLHG-TVVEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 7/89 (7%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
                        L++ N+ F   +  +R+ F + G I  V +   +         S G+
Sbjct: 19  SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-------SKGF 71

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIE 658
           GFV F      ++A + L  + ++  +IE
Sbjct: 72  GFVTFENSADADRAREKLHGTVVEGRKIE 100

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 44.6 bits (106), Expect = 6e-06
 Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           ++     L+  F + G + DV++ +   G  + F F+ +     A  A +  + T V   
Sbjct: 39  FRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEGR 97

Query: 87  RIKVEK 92
           +I+V  
Sbjct: 98  KIEVNN 103

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 13/79 (16%)

Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------- 485
            +    N   +++ KR+  V N+P+R    DL+ +F  FG +  V +    I        
Sbjct: 16  PRGSHMNTENKSQPKRL-HVSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKG 70

Query: 486 -GLVEFLQKNQAKAAFNSL 503
            G V F     A  A   L
Sbjct: 71  FGFVTFENSADADRAREKL 89

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 76.9 bits (190), Expect = 2e-17
 Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 5/89 (5%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           ++ +  +  +  +NLS+ +TED+L ++FE      E+   +  +  K+KG A + F    
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDAL---EIR--LVSQDGKSKGIAYIEFKSEA 64

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            A +  +   G    GR + L     K  
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 18/97 (18%), Positives = 47/97 (48%), Gaps = 7/97 (7%)

Query: 670 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 729
           +  ++   ++   +    +L +N+ F   + E++E+F+   E++ V         G  +G
Sbjct: 1   SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS------QDGKSKG 54

Query: 730 FGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
             ++EF ++ +A++ ++   Q   + GR + L +  E
Sbjct: 55  IAYIEFKSEADAEKNLEEK-QGAEIDGRSVSLYYTGE 90

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 64.2 bits (157), Expect = 6e-13
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 11/98 (11%)

Query: 567 ENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
             +E+    +      TL  KNL+FN TED ++  F+    I  V+   K          
Sbjct: 2   HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK---------- 51

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
           S G  +++F +     + L+  Q + +D   + L  + 
Sbjct: 52  SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 89

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 44.6 bits (106), Expect = 6e-06
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          + IT+++LK  FE+   +  V    + +GK +  A+I +  E  A+  L+      +   
Sbjct: 26 FNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR 81

Query: 87 RIKVEK 92
           + +  
Sbjct: 82 SVSLYY 87

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 11/67 (16%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFG------DLGRVLVPPYGITGLVEFLQKNQA 496
           + R+ R +L KNL +     +LK +FE           G+      GI   +EF  +  A
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK----SKGI-AYIEFKSEADA 66

Query: 497 KAAFNSL 503
           +      
Sbjct: 67  EKNLEEK 73

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 78.6 bits (194), Expect = 2e-17
 Identities = 29/123 (23%), Positives = 48/123 (39%)

Query: 304 ADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPL 363
            D     +      +  +      Q   +      + V  +  TV E  L +LFE+YGP+
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69

Query: 364 AEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVD 423
             V +  D+ET +++G+  V F     A QA   L+G   L + L +           + 
Sbjct: 70  ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA 129

Query: 424 GKV 426
           G V
Sbjct: 130 GAV 132

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 66.7 bits (163), Expect = 3e-13
 Identities = 22/123 (17%), Positives = 53/123 (43%), Gaps = 5/123 (4%)

Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
           +  +  + +   +     N        ++V  IP    + ++ +LF+ +G ++ V++   
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA---EEADNVEDIRKRT 777
              +   RG+GFV+F + + A++A+  L    ++  +RL +  A    +   +       
Sbjct: 78  RE-TRQSRGYGFVKFQSGSSAQQAIAGL-NGFNILNKRLKVALAASGHQRPGIAGAVGDG 135

Query: 778 NRY 780
           N Y
Sbjct: 136 NGY 138

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 55.5 bits (134), Expect = 3e-09
 Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 11/102 (10%)

Query: 552 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 611
              ++  QQ +P  + N       EP+    L +  +     E  +R+ F++ GPI SV 
Sbjct: 20  QQLQQQQQQHIPPTQMN------PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK 73

Query: 612 VARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
           +   ++     Q  S GYGFV+F +  S  QA+  L   ++ 
Sbjct: 74  IVCDRE---TRQ--SRGYGFVKFQSGSSAQQAIAGLNGFNIL 110

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 46.7 bits (111), Expect = 2e-06
 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
             + + QL+  FE  G +  V++   + T   + R + F+ +     AQ A+   N   +
Sbjct: 52  TTVDEVQLRQLFERYGPIESVKIVCDRET--RQSRGYGFVKFQSGSSAQQAIAGLNGFNI 109

Query: 84  FSSRIKV 90
            + R+KV
Sbjct: 110 LNKRLKV 116

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 79.5 bits (196), Expect = 2e-17
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 1/95 (1%)

Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
           +      E +    ++ V NL + V++ D+ +LF ++G L +  +  D  + ++ G A V
Sbjct: 76  DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADV 134

Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            F     A +A +   G    GR + +     + +
Sbjct: 135 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 70.6 bits (173), Expect = 3e-14
 Identities = 26/107 (24%), Positives = 44/107 (41%), Gaps = 3/107 (2%)

Query: 660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK 719
            +   +                 +TG+K+LV N+ F    ++++ELF  FG LK   +  
Sbjct: 63  PKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDY 122

Query: 720 KMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
               SG   G   V F  + +A +AMK   +   L GR + ++    
Sbjct: 123 D--RSGRSLGTADVHFERRADALKAMKQY-KGVPLDGRPMDIQLVAS 166

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 63.7 bits (155), Expect = 8e-12
 Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 6/96 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
              E    L + NL+F  ++  I+  F + G +    V   +     G+  S+G   V F
Sbjct: 83  EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS----GR--SLGTADVHF 136

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA 670
             R    +A+K  +   LD   ++++     ++ E 
Sbjct: 137 ERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 172

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 58.3 bits (141), Expect = 5e-10
 Identities = 10/65 (15%), Positives = 26/65 (40%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           + ++   ++  F E GT+    + Y   G+    A + + R   A  A+  +    +   
Sbjct: 98  FGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR 157

Query: 87  RIKVE 91
            + ++
Sbjct: 158 PMDIQ 162

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 46.4 bits (110), Expect = 7e-06
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 504
           +LV NL +     D++ LF  FG L +  V     G    T  V F ++  A  A     
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150

Query: 505 YTKFKEVPLYLEWAPE 520
                  P+ ++    
Sbjct: 151 GVPLDGRPMDIQLVAS 166

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 40.2 bits (94), Expect = 8e-04
 Identities = 17/98 (17%), Positives = 30/98 (30%), Gaps = 8/98 (8%)

Query: 200 KSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF- 257
           K                          ++V NL  GV   D++  F     L      + 
Sbjct: 64  KPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 123

Query: 258 -----LGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNI 289
                LG A + F+   +  KA+ +       G+ ++I
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 76.9 bits (190), Expect = 3e-17
 Identities = 30/87 (34%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
           S   S  F         +FV NL   V E+ L +LF + GPL +V +  D+E  K K F 
Sbjct: 2   SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFG 60

Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRML 408
            V F  PE  + A   L+G    GR +
Sbjct: 61  FVCFKHPESVSYAIALLNGIRLYGRPI 87

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 69.2 bits (170), Expect = 1e-14
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
             + E D T+++ NL     E+ +   F + GP+  VT+ + ++ K         +GFV 
Sbjct: 10  PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK------PKSFGFVC 63

Query: 634 FYTRESLNQALKVLQNSSLD 653
           F   ES++ A+ +L    L 
Sbjct: 64  FKHPESVSYAIALLNGIRLY 83

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 64.2 bits (157), Expect = 7e-13
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
           ++    + V N+  + ++  + ELF   G L  V + K     G  + FGFV F      
Sbjct: 13  EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD--REGKPKSFGFVCFKHPESV 70

Query: 742 KRAMKALCQSTHLYGRRLVLEWA 764
             A+  L     LYGR + +   
Sbjct: 71  SYAIALL-NGIRLYGRPINVSGP 92

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 16/69 (23%), Positives = 30/69 (43%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           ++ +E L   F + G +T V +    EGK + F F+ +   +    A+   N   ++  
Sbjct: 26 ARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGR 85

Query: 87 RIKVEKCSN 95
           I V   S+
Sbjct: 86 PINVSGPSS 94

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 7/85 (8%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQA 496
           +  + R + V NL  R     L  LF   G L +V +       P    G V F      
Sbjct: 12  QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSF-GFVCFKHPESV 70

Query: 497 KAAFNSLAYTKFKEVPLYLEWAPEG 521
             A   L   +    P+ +     G
Sbjct: 71  SYAIALLNGIRLYGRPINVSGPSSG 95

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 81.8 bits (201), Expect = 3e-17
 Identities = 46/329 (13%), Positives = 87/329 (26%), Gaps = 64/329 (19%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKTKGFALVTF 385
             +   +  I++ NL+  + +D+L K    +F ++G + ++++     + K +G A V F
Sbjct: 3   VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIF 59

Query: 386 LMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEAR 445
                AT A + + G  F  + + +   K                S+         VE  
Sbjct: 60  KEVSSATNALRSMQGFPFYDKPMRIQYAKTD--------------SDIIAKMKGTFVERD 105

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY 505
            KR    K  P        K   +  G    V      + G+    Q  +          
Sbjct: 106 RKR---EKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMP---- 158

Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
                                     G+                                
Sbjct: 159 --------------------------GQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMP 192

Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
            +        E  P+  L++ NL   + E  +   F +      V +   +         
Sbjct: 193 GQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH-------- 244

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE 654
                FV+F        A   LQ   + +
Sbjct: 245 --DIAFVEFDNEVQAGAARDALQGFKITQ 271

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 66.1 bits (160), Expect = 7e-12
 Identities = 50/329 (15%), Positives = 88/329 (26%), Gaps = 60/329 (18%)

Query: 443 EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 495
           E R    I + NL  +    +LK    A+F  FG +  +LV           V F + + 
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 496 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAE 555
           A  A  S+    F + P+ +++A      +       K K    E   + E+ K ++   
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYA------KTDSDIIAKMKGTFVERDRKREKRKPKSQET 118

Query: 556 EDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 615
              ++ V                                 +++       P+        
Sbjct: 119 PATKKAVQ-----------------------GGGATPVVGAVQGPVPGMPPMTQAPRIMH 155

Query: 616 KDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKR 675
             P  P      G           +       Q     +                     
Sbjct: 156 HMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMP------------------P 197

Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
                       + + N+P +  +  +  LF  F   K VRL              FVEF
Sbjct: 198 AQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG------RHDIAFVEF 251

Query: 736 ITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
             + +A  A  AL          + + +A
Sbjct: 252 DNEVQAGAARDALQGFKITQNNAMKISFA 280

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 60.7 bits (146), Expect = 4e-10
 Identities = 38/279 (13%), Positives = 88/279 (31%), Gaps = 27/279 (9%)

Query: 27  YKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
            KI +++LK    A F + G + D+ +  +   K R  AF+ +     A  AL       
Sbjct: 19  EKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKEVSSATNALRSMQGFP 76

Query: 83  VFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSA--YQKLHNIAPKQDLKPEHTKDSKPGKK 140
            +   ++++             ++K   D  A           K++ +   ++++   KK
Sbjct: 77  FYDKPMRIQ-------------YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKK 123

Query: 141 SKNDPTFSDFLQLHGKDVSKLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTK 200
           +      +  +      V  + P++           +              +   ++   
Sbjct: 124 AVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPG 183

Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLP---LASVRTTF 257
           +       P   P ++        H + + NLP    +  L   F   P      +    
Sbjct: 184 AMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR 243

Query: 258 LGMAYIGFKDEKNCNKALNK--NKSFWKGKQLNIYKYSK 294
             +A++ F +E     A +        +   + I  ++K
Sbjct: 244 HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI-SFAK 281

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 57.6 bits (138), Expect = 4e-09
 Identities = 18/87 (20%), Positives = 44/87 (50%), Gaps = 9/87 (10%)

Query: 688 ILVRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           I + N+  + K+ E+++    +F  FG++  + + +    S   RG  FV F   + A  
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR----SLKMRGQAFVIFKEVSSATN 67

Query: 744 AMKALCQSTHLYGRRLVLEWAEEADNV 770
           A++++ Q    Y + + +++A+   ++
Sbjct: 68  ALRSM-QGFPFYDKPMRIQYAKTDSDI 93

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 54.9 bits (131), Expect = 3e-08
 Identities = 53/324 (16%), Positives = 88/324 (27%), Gaps = 57/324 (17%)

Query: 207 SDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-----PLASVRT----TF 257
           + P   P           HTI + NL   +KK +LK     +      +  +        
Sbjct: 2   AVPETRPN----------HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM 51

Query: 258 LGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIK 316
            G A++ FK+  +   AL       +  K + I +Y+K +S   +           +  K
Sbjct: 52  RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI-QYAKTDSDIIAKMKGTFVERDRKREK 110

Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK 376
            K    +  + + A                           +  G    V          
Sbjct: 111 RKPKSQETPATKKA--------------------------VQGGGATPVVGAVQGPVPGM 144

Query: 377 TKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLD 436
                    +        Y    G +    +       P                 + L 
Sbjct: 145 PPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAP--GQIPPGAMPPQQLMPGQMPPAQPLS 202

Query: 437 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL-GRVLVPPYGITGLVEFLQKNQ 495
                       I+ + NLP  T    L  LF  F       LVP       VEF  + Q
Sbjct: 203 ENPP------NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQ 256

Query: 496 AKAAFNSLAYTKF-KEVPLYLEWA 518
           A AA ++L   K  +   + + +A
Sbjct: 257 AGAARDALQGFKITQNNAMKISFA 280

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 75.8 bits (187), Expect = 5e-17
 Identities = 19/76 (25%), Positives = 31/76 (40%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
               I V+N+ +TV+ D++   F  Y  +   +     E     G A+V F   + AT A
Sbjct: 14  GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 395 YQHLDGTVFLGRMLHL 410
              L+      R + L
Sbjct: 74  VIDLNDRPIGSRKVKL 89

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 65.4 bits (160), Expect = 3e-13
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEF 735
            S+  K   + I V+N+PF     E+ + F  +  +   V L       G+  G   V F
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EKGMPTGEAMVAF 64

Query: 736 ITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
            +++EA  A+  L     +  R++ L   
Sbjct: 65  ESRDEATAAVIDL-NDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 63.9 bits (156), Expect = 9e-13
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
               T + ++N+ F  + D I   F     I    V  K + K  G     G   V F +
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGS-VCLKYNEK--GM--PTGEAMVAFES 66

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSN 663
           R+    A+  L +  +   +++L   +
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVKLSGPS 93

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          + ++ +++   F     +   V LKY  +G     A + +   D+A AA+   N+  + S
Sbjct: 25 FTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS 84

Query: 86 SRIKVEKCS 94
           ++K+   S
Sbjct: 85 RKVKLSGPS 93

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 499
              +I V+N+P+     ++   F  +  +   +   Y   G      +V F  +++A AA
Sbjct: 14  GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 500 FNSLAYTKFKEVPLYLEWAPEG 521
              L         + L     G
Sbjct: 74  VIDLNDRPIGSRKVKLSGPSSG 95

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 12/79 (15%), Positives = 25/79 (31%), Gaps = 9/79 (11%)

Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALN 276
             I V+N+P  V   ++  +F    +                G A + F+       A+ 
Sbjct: 16  TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 277 K-NKSFWKGKQLNIYKYSK 294
             N      +++ +   S 
Sbjct: 76  DLNDRPIGSRKVKLSGPSS 94

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 75.8 bits (187), Expect = 6e-17
 Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 8/90 (8%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           +  +A+   +FVRNL+ TVTE+ L K F ++G L  V         K K +A + F   +
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERD 56

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            A +A + ++G    G  + ++  KP + +
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVFAKPPDQK 86

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 17/109 (15%), Positives = 40/109 (36%), Gaps = 13/109 (11%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
                 L+++NL    TE+ + + F + G +  V   +              Y F+ F  
Sbjct: 8   MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------------DYAFIHFDE 54

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
           R+   +A++ +    L+   IE+  +    +       ++ +     +G
Sbjct: 55  RDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 60.8 bits (148), Expect = 1e-11
 Identities = 22/103 (21%), Positives = 43/103 (41%), Gaps = 10/103 (9%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
           S +        + VRN+     +  +E+ F  FG+L+ V+  K          + F+ F 
Sbjct: 3   SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---------DYAFIHFD 53

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
            ++ A +AM+ +     L G  + + +A+  D     RK   +
Sbjct: 54  ERDGAVKAMEEM-NGKDLEGENIEIVFAKPPDQKRKERKAQRQ 95

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 47.3 bits (113), Expect = 8e-07
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 7/65 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            +T+E L+  F + G +  V+       K + +AFI +   D A  A++  N   +   
Sbjct: 21 NTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNGKDLEGE 73

Query: 87 RIKVE 91
           I++ 
Sbjct: 74 NIEIV 78

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 12/99 (12%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-PYGITGLVEFLQKNQAKAAFNSLAYT 506
           +++ V+NL        L+  F  FG L RV     Y     + F +++ A  A   +   
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY---AFIHFDERDGAVKAMEEMNGK 68

Query: 507 KFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEG 545
             +   + + +        AK   + +++ K + +   G
Sbjct: 69  DLEGENIEIVF--------AKPPDQKRKERKAQRQAASG 99

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 75.4 bits (186), Expect = 7e-17
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 7/81 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++++ NLS  VT DDL +LF          LP+  +     G+A V +     A +A + 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 398 LDGTV-FLGRMLHLIPGKPKE 417
           L G V   G+++ +     K+
Sbjct: 64  LSGKVELHGKIMEVDYSVSKK 84

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 15/79 (18%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           +K+ + N+       ++ +LF         ++        L  G+ FV++  +N A RA+
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-------LLKSGYAFVDYPDQNWAIRAI 61

Query: 746 KALCQSTHLYGRRLVLEWA 764
           + L     L+G+ + ++++
Sbjct: 62  ETLSGKVELHGKIMEVDYS 80

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 11/71 (15%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
                 LYI NL+   T D +R+ F       +  V  K            GY FV +  
Sbjct: 5   SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----------GYAFVDYPD 53

Query: 637 RESLNQALKVL 647
           +    +A++ L
Sbjct: 54  QNWAIRAIETL 64

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 10/67 (14%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            +T + L+  F ++      Q+          +AF+ Y  ++ A  A++  +       
Sbjct: 18 PAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLSGKVELHG 72

Query: 87 R-IKVEK 92
          + ++V+ 
Sbjct: 73 KIMEVDY 79

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 75.3 bits (186), Expect = 7e-17
 Identities = 20/75 (26%), Positives = 34/75 (45%)

Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
            +     +FV +LS  +T   +   F  +G +++  +  D  T K+KG+  V+F     A
Sbjct: 2   PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61

Query: 392 TQAYQHLDGTVFLGR 406
             A Q + G    GR
Sbjct: 62  ENAIQQMGGQWLGGR 76

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 55.6 bits (135), Expect = 6e-10
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           +   + V ++  +   + +   F  FG +   R+ K M  +G  +G+GFV F  K +A+ 
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAEN 63

Query: 744 AMKALCQSTHLYGRRLVLEWAEE 766
           A++ +     L GR++   WA  
Sbjct: 64  AIQQM-GGQWLGGRQIRTNWATR 85

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
                 +++ +L+   T  +I   F   G I+   V +  D  + G+  S GYGFV F+ 
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVK--DMAT-GK--SKGYGFVSFFN 57

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNR 664
           +     A++ +    L   QI    + R
Sbjct: 58  KWDAENAIQQMGGQWLGGRQIRTNWATR 85

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 7  GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGY 65
          GP+    H+ + DL       +IT   + A F   G ++D ++      GK + + F+ +
Sbjct: 1  GPLGSHFHVFVGDLS-----PEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSF 55

Query: 66 HREDQAQAALDYFNNTYVFSSRIKV 90
            +  A+ A+      ++   +I+ 
Sbjct: 56 FNKWDAENAIQQMGGQWLGGRQIRT 80

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 75.4 bits (186), Expect = 8e-17
 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +++V NL     + +L + F  YGPL  V +  +       GFA V F  P  A  A + 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56

Query: 398 LDGTVFLGRML 408
           LDG V  G  +
Sbjct: 57  LDGKVICGSRV 67

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 68.9 bits (169), Expect = 2e-14
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ V N+   A + E+E  F  +G L+ V + +         GF FVEF    +A+ A++
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP------PGFAFVEFEDPRDAEDAVR 55

Query: 747 ALCQSTHLYGRRLVLEWAEE 766
            L     + G R+ +E +  
Sbjct: 56  GL-DGKVICGSRVRVELSTG 74

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 55.4 bits (134), Expect = 9e-10
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 10/71 (14%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +Y+ NL   + +  + R F   GP+ +V +   ++P         G+ FV+F        
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWI--ARNPP--------GFAFVEFEDPRDAED 52

Query: 643 ALKVLQNSSLD 653
           A++ L    + 
Sbjct: 53  AVRGLDGKVIC 63

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 4/65 (6%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
              + +L+  F   G +  V +     G    FAF+ +     A+ A+   +   +  S
Sbjct: 10 TGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLDGKVICGS 65

Query: 87 RIKVE 91
          R++VE
Sbjct: 66 RVRVE 70

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 3/69 (4%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
           V NL       +L+  F  +G L  V +   P G    VEF     A+ A   L      
Sbjct: 5   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGF-AFVEFEDPRDAEDAVRGLDGKVIC 63

Query: 510 EVPLYLEWA 518
              + +E +
Sbjct: 64  GSRVRVELS 72

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 79.0 bits (194), Expect = 1e-16
 Identities = 24/145 (16%), Positives = 53/145 (36%), Gaps = 3/145 (2%)

Query: 275 LNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNA-SMENIKAKHWKSQEDSVQFAEDI 333
            N+   +    Q+++Y      SA    A +D +   ++                     
Sbjct: 6   FNQEAEYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYT 65

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGP--LAEVILPIDKETDKTKGFALVTFLMPEHA 391
            +   +++ NL++  T++DLT+     G   + E+    ++   ++KGFALV       +
Sbjct: 66  GKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASS 125

Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPK 416
            +    L      G+   + P   +
Sbjct: 126 KKLMDLLPKRELHGQNPVVTPVNKQ 150

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 62.0 bits (150), Expect = 7e-11
 Identities = 22/145 (15%), Positives = 47/145 (32%), Gaps = 3/145 (2%)

Query: 541 EGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH 600
                  E ++         G    +                LYI NL + +T++ +   
Sbjct: 29  ANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEA 88

Query: 601 FKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK 660
               G    + +   ++  + GQ  S G+  V   +  S  + + +L    L      + 
Sbjct: 89  VHSLGVNDILEIKFFENRAN-GQ--SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT 145

Query: 661 RSNRNLESEATTVKRKSSNVAKQTG 685
             N+   S+     RK++   + +G
Sbjct: 146 PVNKQFLSQFEMQSRKTTQSGQMSG 170

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 56.6 bits (136), Expect = 4e-09
 Identities = 18/128 (14%), Positives = 45/128 (35%), Gaps = 9/128 (7%)

Query: 646 VLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGS-----KILVRNIPFQAKQS 700
           V+  S+ +    E +     L         K +              + + N+ +     
Sbjct: 24  VISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDE 83

Query: 701 EVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR 758
           ++ E   + G  ++  ++  +    +G  +GF  V   ++  +K+ M  L     L+G+ 
Sbjct: 84  DLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKKLMDLL-PKRELHGQN 141

Query: 759 LVLEWAEE 766
            V+    +
Sbjct: 142 PVVTPVNK 149

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 40.9 bits (95), Expect = 7e-04
 Identities = 12/71 (16%), Positives = 25/71 (35%), Gaps = 3/71 (4%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTE---GKFRRFAFIGYHREDQAQAALDYFNNTYV 83
           +  T E L       G    +++K+      G+ + FA +G   E  ++  +D      +
Sbjct: 78  WWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL 137

Query: 84  FSSRIKVEKCS 94
                 V   +
Sbjct: 138 HGQNPVVTPVN 148

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 74.7 bits (184), Expect = 1e-16
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 2/69 (2%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYG--PLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
               I +RN++     D +      Y    +  + L  DK+T + +GFA V       A+
Sbjct: 8   HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDAS 67

Query: 393 QAYQHLDGT 401
           Q  Q L   
Sbjct: 68  QLLQILQSL 76

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 67.7 bits (166), Expect = 4e-14
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
                 T+ ++N+  ++  DSI         +A   +   KD ++     + G+ FVQ  
Sbjct: 5   HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQ---QNRGFAFVQLS 61

Query: 636 TRESLNQALKVLQNS----SLDEHQIELKRSNR 664
           +    +Q L++LQ+      +D   I +  +  
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAK 742
              I++RNI        +      +  L    +RL K    +  +RGF FV+  +  +A 
Sbjct: 9   MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQ-TQQNRGFAFVQLSSAMDAS 67

Query: 743 RAMKAL---CQSTHLYGRRLVLEWAEEA 767
           + ++ L        + G+ + +++A+ A
Sbjct: 68  QLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 12/76 (15%), Positives = 23/76 (30%), Gaps = 11/76 (14%)

Query: 27 YKITQEQLKAKFEEKGT--VTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
               + +        +  V +++L   K T   + R FAF+       A   L    + 
Sbjct: 19 PHTVVDSIMTALSPYASLAVNNIRLIKDKQT--QQNRGFAFVQLSSAMDASQLLQILQSL 76

Query: 82 YVFSS----RIKVEKC 93
          +         I V+  
Sbjct: 77 HPPLKIDGKTIGVDFA 92

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 74.2 bits (183), Expect = 2e-16
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
             + +IFV N+S   T  +L  LFE+ G + E  +         K +A V       A  
Sbjct: 7   GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKA 58

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKE 417
           A   L+G    G+ +++      +
Sbjct: 59  AIAQLNGKEVKGKRINVELSTKGQ 82

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 10/89 (11%)

Query: 678 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 737
           S+ +     KI V N+       E+  LF+  G +             + + + FV    
Sbjct: 2   SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECD---------VVKDYAFVHMEK 52

Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           + +AK A+  L     + G+R+ +E + +
Sbjct: 53  EADAKAAIAQL-NGKEVKGKRINVELSTK 80

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 55.3 bits (134), Expect = 9e-10
 Identities = 12/84 (14%), Positives = 25/84 (29%), Gaps = 13/84 (15%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                   +++ N++   T   +R  F++ G +    V +              Y FV  
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------------DYAFVHM 50

Query: 635 YTRESLNQALKVLQNSSLDEHQIE 658
                   A+  L    +   +I 
Sbjct: 51  EKEADAKAAIAQLNGKEVKGKRIN 74

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 49.5 bits (119), Expect = 7e-08
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
              T ++L++ FE +G V +  +        + +AF+   +E  A+AA+   N   V   
Sbjct: 19  AACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGK 71

Query: 87  RIKVEKCSNLGDTTKPKS 104
           RI VE  +     + P S
Sbjct: 72  RINVELSTKGQKKSGPSS 89

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 74.4 bits (183), Expect = 3e-16
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
               ++ +  IP   K+ E+ E      E +  V +         +RGF FVE+ +   A
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 742 KRAMKALCQSTH-LYGRRLVLEWAEEADNVED 772
             A + L      L+G ++ ++WAE   +V++
Sbjct: 66  AMARRKLMPGRIQLWGHQIAVDWAEPEIDVDE 97

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 60.2 bits (146), Expect = 3e-11
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGP-LAEVILPID-KETDKTKGFALVTFLMPEHAT 392
            + R+F+  +      +++ +   K    + +VI+     +  K +GFA V +     A 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 393 QAYQHL--DGTVFLGRML 408
            A + L        G  +
Sbjct: 67  MARRKLMPGRIQLWGHQI 84

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.7 bits (142), Expect = 8e-11
 Identities = 16/104 (15%), Positives = 36/104 (34%), Gaps = 7/104 (6%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
             +  L+I  +      + I     K    +  V V          +  + G+ FV++ +
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIV--YASAADKMK--NRGFAFVEYES 61

Query: 637 RESLNQALKVLQNSS--LDEHQIELKRSNRNLESEATTVKRKSS 678
             +   A + L      L  HQI +  +   ++ +   ++  S 
Sbjct: 62  HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSG 105

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 14/70 (20%), Positives = 26/70 (37%), Gaps = 5/70 (7%)

Query: 27 YKITQEQLKAKFEEKGT-VTDVQLKY--TTEGKFRRFAFIGYHREDQAQAALDYFNN--T 81
              +E++  +  +    V DV +      + K R FAF+ Y     A  A         
Sbjct: 18 KMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRI 77

Query: 82 YVFSSRIKVE 91
           ++  +I V+
Sbjct: 78 QLWGHQIAVD 87

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 73.9 bits (182), Expect = 4e-16
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            ++   ++  +T+  + + F  +G + E+ +  +      KG++ V F   E A  A   
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80

Query: 398 LDGTVFLGRMLHLIPGKPKEN 418
           ++GT   G ++    GK   +
Sbjct: 81  VNGTTIEGHVVKCYWGKESPD 101

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.9 bits (169), Expect = 2e-14
 Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 11/100 (11%)

Query: 558 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 617
           +       +   E+   +    + T+Y   +    T+  +R+ F   G I  + V  +K 
Sbjct: 3   SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK- 61

Query: 618 PKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
                     GY FV+F T ES   A+  +  ++++ H +
Sbjct: 62  ----------GYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.7 bits (158), Expect = 6e-13
 Identities = 20/100 (20%), Positives = 38/100 (38%), Gaps = 11/100 (11%)

Query: 668 SEATTVKRKSSNVAKQTGSK---ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 724
           S   T + +  +V  Q+  K   +    I        + + F  FG++  +R+       
Sbjct: 5   SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP----- 59

Query: 725 GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
              +G+ FV F T   A  A+ ++   T + G  +   W 
Sbjct: 60  --EKGYSFVRFSTHESAAHAIVSV-NGTTIEGHVVKCYWG 96

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.0 bits (107), Expect = 5e-06
 Identities = 13/88 (14%), Positives = 34/88 (38%), Gaps = 18/88 (20%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             +T + ++  F   G + ++++        + ++F+ +   + A  A+   N T +   
Sbjct: 35  SGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNGTTIEGH 89

Query: 87  RIKVEKCSNLGDTTKPKSWSKYAPDSSA 114
            +K               W K +PD ++
Sbjct: 90  VVKC-------------YWGKESPDMTS 104

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 14/69 (20%), Positives = 22/69 (31%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 511
              +        ++  F PFG +  + V P      V F     A  A  S+  T  +  
Sbjct: 30  CGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGH 89

Query: 512 PLYLEWAPE 520
            +   W  E
Sbjct: 90  VVKCYWGKE 98

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 73.0 bits (180), Expect = 4e-16
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++F+ NL    TE ++  LFE+YG + E  +         K +  V       A  A ++
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61

Query: 398 LDGTVFLGRMLHLIPGKPKE 417
           L      G  +++   K K 
Sbjct: 62  LHHYKLHGVNINVEASKNKS 81

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 67.6 bits (166), Expect = 4e-14
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            K+ + N+P +A + E+  LF+ +G++    + K          +GFV    K  A+ A+
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK---------NYGFVHIEDKTAAEDAI 59

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
           + L     L+G  + +E ++ 
Sbjct: 60  RNL-HHYKLHGVNINVEASKN 79

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 13/77 (16%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
             L+I NL   +TE  IR  F++ G +    + +              YGFV    + + 
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK-------------NYGFVHIEDKTAA 55

Query: 641 NQALKVLQNSSLDEHQI 657
             A++ L +  L    I
Sbjct: 56  EDAIRNLHHYKLHGVNI 72

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 48.3 bits (116), Expect = 2e-07
 Identities = 11/66 (16%), Positives = 30/66 (45%), Gaps = 7/66 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
           + T++++++ FE+ G V +  +        + + F+    +  A+ A+   ++  +   
Sbjct: 18 REATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGV 70

Query: 87 RIKVEK 92
           I VE 
Sbjct: 71 NINVEA 76

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNS 502
           +     + + NLP      ++++LFE +G +    ++  Y   G V    K  A+ A  +
Sbjct: 5   SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY---GFVHIEDKTAAEDAIRN 61

Query: 503 LAYTKFKEVPLYLEWA 518
           L + K   V + +E +
Sbjct: 62  LHHYKLHGVNINVEAS 77

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 73.4 bits (181), Expect = 4e-16
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
            ED  +   ++V NLS  VTE  + +LF + GP     +  +  ++    +  V F    
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHR 66

Query: 390 HATQAYQHLDGTVFLGR 406
            A  A   ++G   LG+
Sbjct: 67  DAAAALAAMNGRKILGK 83

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
               + V N+     +  + +LF   G  K  ++  +      +  + FVEF    +A  
Sbjct: 14  QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS---NDPYCFVEFYEHRDAAA 70

Query: 744 AMKALCQSTHLYGRRLVLEWA 764
           A+ A+     + G+ + + WA
Sbjct: 71  ALAAM-NGRKILGKEVKVNWA 90

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.7 bits (148), Expect = 1e-11
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           +     TLY+ NL+ + TE  I + F + GP  S  +  +     P       Y FV+FY
Sbjct: 11  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-------YCFVEFY 63

Query: 636 TRESLNQALKVLQNSSLDEHQI 657
                  AL  +    +   ++
Sbjct: 64  EHRDAAAALAAMNGRKILGKEV 85

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 4/84 (4%)

Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL----VEFLQKN 494
             + +    R + V NL        +  LF   G      +     +      VEF +  
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 495 QAKAAFNSLAYTKFKEVPLYLEWA 518
            A AA  ++   K     + + WA
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWA 90

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 1/64 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            +T+  +   F + G     ++          + F+ ++    A AAL   N   +   
Sbjct: 25 RDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNGRKILGK 83

Query: 87 RIKV 90
           +KV
Sbjct: 84 EVKV 87

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 75.0 bits (184), Expect = 6e-16
 Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGP--LAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
              ++V + S+  T+  L ++    G   + E+    ++   ++KG+A V         +
Sbjct: 55  RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114

Query: 394 AYQHLDGTVFLGRML 408
             + L G V  G  +
Sbjct: 115 LLELLPGKVLNGEKV 129

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 57.6 bits (139), Expect = 7e-10
 Identities = 14/111 (12%), Positives = 42/111 (37%), Gaps = 6/111 (5%)

Query: 659 LKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP 718
           +++      +  T     + +  +   + + V +  +     ++ ++ ++ G    V L 
Sbjct: 29  VRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL- 87

Query: 719 KKMV---GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
            K      +G  +G+  V   ++N   + ++ L     L G ++ +  A  
Sbjct: 88  -KFAENRANGQSKGYAEVVVASENSVHKLLELL-PGKVLNGEKVDVRPATR 136

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 53.4 bits (128), Expect = 2e-08
 Identities = 17/131 (12%), Positives = 46/131 (35%), Gaps = 13/131 (9%)

Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
                     +    +  E     ++E + + +N+         +             +Y
Sbjct: 6   HHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTP------AILYTYSGLRNRRAAVY 59

Query: 585 IKNLNFNSTEDSIRRHFKKCGP--IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           + + ++ +T+  + +  +  G   +  +  A  +     GQ  S GY  V   +  S+++
Sbjct: 60  VGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA---NGQ--SKGYAEVVVASENSVHK 114

Query: 643 ALKVLQNSSLD 653
            L++L    L+
Sbjct: 115 LLELLPGKVLN 125

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 73.1 bits (180), Expect = 7e-16
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 4/91 (4%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
            S        K+ V  +  Q  + +V  LF+ FG +    + +     G  +G  FV+F 
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG--PDGSSKGCAFVKFS 64

Query: 737 TKNEAKRAMKALCQSTHLYG--RRLVLEWAE 765
           +  EA+ A+ AL  S  + G    LV+++A+
Sbjct: 65  SHTEAQAAIHALHGSQTMPGASSSLVVKFAD 95

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 66.9 bits (164), Expect = 1e-13
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
               ++FV  L+   +E+D+ +LF+ +G + E  +        +KG A V F     A  
Sbjct: 13  GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQA 71

Query: 394 AYQHLDGTVFL 404
           A   L G+  +
Sbjct: 72  AIHALHGSQTM 82

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 65.4 bits (160), Expect = 3e-13
 Identities = 22/83 (26%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
             E     D  L++  LN   +E+ + R F+  G I   TV R  D  S       G  F
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK------GCAF 60

Query: 632 VQFYTRESLNQALKVLQNSSLDE 654
           V+F +      A+  L  S    
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMP 83

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF-- 84
           + ++E +   F+  G + +  +    +G  +  AF+ +    +AQAA+   + +     
Sbjct: 25 KQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG 84

Query: 85 -SSRIKV 90
           SS + V
Sbjct: 85 ASSSLVV 91

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 41.5 bits (98), Expect = 9e-05
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLG--RVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 506
           V  L  +    D+  LF+PFG +    VL  P G +     V+F    +A+AA ++L  +
Sbjct: 20  VGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79

Query: 507 KFKE---VPLYLEWA 518
           +        L +++A
Sbjct: 80  QTMPGASSSLVVKFA 94

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 72.7 bits (179), Expect = 7e-16
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
               +V NL +   + D+  +F+    +  V L  DK+TDK KGF  V F   +   +A 
Sbjct: 15  PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73

Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGN 421
              DG +   R L +   + ++ + +
Sbjct: 74  T-YDGALLGDRSLRVDIAEGRKQDKS 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 58.4 bits (142), Expect = 9e-11
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           EP  T Y+ NL FN+ +  I   FK    I SV + R KD          G+ +V+F   
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKF-----KGFCYVEFDEV 66

Query: 638 ESLNQALKVLQNSSLDEHQI 657
           +SL +AL     + L +  +
Sbjct: 67  DSLKEALT-YDGALLGDRSL 85

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 54.2 bits (131), Expect = 3e-09
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
              V N+PF   Q +++ +FK    ++ VRL +    +   +GF +VEF   +  K A+ 
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK-DTDKFKGFCYVEFDEVDSLKEALT 74

Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
                  L  R L ++ AE    
Sbjct: 75  Y--DGALLGDRSLRVDIAEGRKQ 95

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 72.5 bits (178), Expect = 8e-16
 Identities = 20/71 (28%), Positives = 30/71 (42%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           +G   + +    V +  LT LF K G +  +  PID+ T KTKGF  V       A +  
Sbjct: 12  NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71

Query: 396 QHLDGTVFLGR 406
           +   G     +
Sbjct: 72  KSFHGKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 47.8 bits (114), Expect = 5e-07
 Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 7/70 (10%)

Query: 685 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 738
              I+V   P          +  +  LF   G++  +  P     +G  +GF FVE  + 
Sbjct: 6   DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA-TGKTKGFLFVECGSM 64

Query: 739 NEAKRAMKAL 748
           N+AK+ +K+ 
Sbjct: 65  NDAKKIIKSF 74

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 5/70 (7%)

Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQA 643
            I +      + ++   F K G + ++       P       + G+ FV+  +     + 
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEF-----PIDEATGKTKGFLFVECGSMNDAKKI 70

Query: 644 LKVLQNSSLD 653
           +K      LD
Sbjct: 71  IKSFHGKRLD 80

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 41.3 bits (97), Expect = 8e-05
 Identities = 10/56 (17%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNT 81
            + ++ L + F + G V +++       GK + F F+     + A+  +  F+  
Sbjct: 22 VPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 72.3 bits (178), Expect = 9e-16
 Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 12/96 (12%)

Query: 563 PEVEENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 621
           P+V     +   R   P  TT YI N+   +TE  +   F+  G I       +K     
Sbjct: 9   PQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK----- 63

Query: 622 GQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
                 G  F+++ T E     +  L N       +
Sbjct: 64  ------GCCFIKYDTHEQAAVCIVALANFPFQGRNL 93

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 71.2 bits (175), Expect = 3e-15
 Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
             ++ N+ +  TE DL  LF+ +G + +     +      KG   + +   E A      
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82

Query: 398 LDGTVFLGRMLHLIPGKPK 416
           L    F GR L    GK +
Sbjct: 83  LANFPFQGRNLRTGWGKER 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 68.5 bits (168), Expect = 2e-14
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 8/88 (9%)

Query: 679 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 738
             A    +   + NIP  A ++++  LF+ FG +   +           +G  F+++ T 
Sbjct: 21  RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-------EKGCCFIKYDTH 73

Query: 739 NEAKRAMKALCQSTHLYGRRLVLEWAEE 766
            +A   + AL  +    GR L   W +E
Sbjct: 74  EQAAVCIVAL-ANFPFQGRNLRTGWGKE 100

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 47.7 bits (114), Expect = 5e-07
 Identities = 11/64 (17%), Positives = 21/64 (32%), Gaps = 5/64 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          +  T+  L   F+  G + D +         +   FI Y   +QA   +    N      
Sbjct: 37 HFATEADLIPLFQNFGFILDFKH-----YPEKGCCFIKYDTHEQAAVCIVALANFPFQGR 91

Query: 87 RIKV 90
           ++ 
Sbjct: 92 NLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 16/67 (23%), Positives = 26/67 (38%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 511
           + N+P+     DL  LF+ FG +      P      +++    QA     +LA   F+  
Sbjct: 32  IGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGR 91

Query: 512 PLYLEWA 518
            L   W 
Sbjct: 92  NLRTGWG 98

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 72.4 bits (178), Expect = 1e-15
 Identities = 19/66 (28%), Positives = 35/66 (53%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++ ++F+  +   + E DL  LFE++G + E+ +  D+ T   KG A +T+   E A +A
Sbjct: 12  DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 395 YQHLDG 400
              L  
Sbjct: 72  QSALHE 77

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 62.7 bits (153), Expect = 3e-12
 Identities = 22/92 (23%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
           SS +      K+ +  IP    + +++ LF+ FG++  + + K    +G+H+G  F+ + 
Sbjct: 5   SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-TGMHKGCAFLTYC 63

Query: 737 TKNEAKRAMKALCQSTHLYG--RRLVLEWAEE 766
            +  A +A  AL +   L G  R + ++ A+ 
Sbjct: 64  ERESALKAQSALHEQKTLPGMNRPIQVKPADS 95

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 25/107 (23%), Positives = 43/107 (40%), Gaps = 12/107 (11%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
              +      L+I  +  N  E  ++  F++ G I  +TV +  D  + G     G  F+
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLK--DRFT-GM--HKGCAFL 60

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE-SEATTVKRKSS 678
            +  RES  +A       +L E +  L   NR ++   A +  R  S
Sbjct: 61  TYCERESALKAQS-----ALHEQKT-LPGMNRPIQVKPADSESRGGS 101

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 8/70 (11%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
            + ++ LK  FEE G + ++ +   ++T  G  +  AF+ Y   + A  A    +    
Sbjct: 23 RNLDEKDLKPLFEEFGKIYELTVLKDRFT--GMHKGCAFLTYCERESALKAQSALHEQKT 80

Query: 84 F---SSRIKV 90
              +  I+V
Sbjct: 81 LPGMNRPIQV 90

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 7/91 (7%)

Query: 332 DIAESGRIFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
           +   +  I++ NL+  + +D+L K    +F ++G + ++++     + K +G A V F  
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKE 60

Query: 388 PEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
              AT A + + G  F  + + +   K   +
Sbjct: 61  VSSATNALRSMQGFPFYDKPMRIQYAKTDSD 91

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 61.1 bits (149), Expect = 9e-12
 Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 690 VRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + N+  + K+ E+++    +F  FG++  + + +    S   RG  FV F   + A  A+
Sbjct: 13  INNLNEKIKKDELKKSLHAIFSRFGQILDILVSR----SLKMRGQAFVIFKEVSSATNAL 68

Query: 746 KALCQSTHLYGRRLVLEWA 764
           +++ Q    Y + + +++A
Sbjct: 69  RSM-QGFPFYDKPMRIQYA 86

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 58.4 bits (142), Expect = 8e-11
 Identities = 27/111 (24%), Positives = 44/111 (39%), Gaps = 23/111 (20%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
           E  P+ T+YI NLN    +D +++     F + G I  + V   +  K  GQ       F
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQ------AF 55

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAK 682
           V F    S   AL+ +Q     +  + ++ +           K  S  +AK
Sbjct: 56  VIFKEVSSATNALRSMQGFPFYDKPMRIQYA-----------KTDSDIIAK 95

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 45.7 bits (109), Expect = 3e-06
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 27 YKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
           KI +++LK    A F   G + D+ +  +   K R  AF+ +     A  AL       
Sbjct: 18 EKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATNALRSMQGFP 75

Query: 83 VFSSRIKVE 91
           +   ++++
Sbjct: 76 FYDKPMRIQ 84

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 15/102 (14%)

Query: 443 EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 495
           E R    I + NL  +    +LK    A+F  FG +  +LV           V F + + 
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63

Query: 496 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEK 537
           A  A  S+    F + P+ +++        AK  S    K K
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQY--------AKTDSDIIAKMK 97

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 71.3 bits (175), Expect = 2e-15
 Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
              ++ +RN+   +  + L  L  +YG +          TD       VT+   + A QA
Sbjct: 14  RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ---VNTDSETAVVNVTYSSKDQARQA 70

Query: 395 YQHLDGTVFLGRMLH 409
              L+G       L 
Sbjct: 71  LDKLNGFQLENFTLK 85

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 59.0 bits (143), Expect = 5e-11
 Identities = 17/100 (17%), Positives = 39/100 (39%), Gaps = 5/100 (5%)

Query: 672 TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 731
           +     S   +Q   K+ +RNIP   +   ++ L   +G ++        V +       
Sbjct: 2   SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ----VNTDSETAVV 57

Query: 732 FVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVE 771
            V + +K++A++A+  L     L    L + +  +    +
Sbjct: 58  NVTYSSKDQARQALDKL-NGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 50.9 bits (122), Expect = 3e-08
 Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 8/83 (9%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           + +    L I+N+  +   + +     + G + S                      V + 
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET--------AVVNVTYS 62

Query: 636 TRESLNQALKVLQNSSLDEHQIE 658
           +++   QAL  L    L+   ++
Sbjct: 63  SKDQARQALDKLNGFQLENFTLK 85

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 49.0 bits (117), Expect = 2e-07
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 3/92 (3%)

Query: 437 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG---DLGRVLVPPYGITGLVEFLQK 493
           +   V + +  R + ++N+P       L +L   +G      +V          V +  K
Sbjct: 5   SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSK 64

Query: 494 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE 525
           +QA+ A + L   + +   L + + P+ + A+
Sbjct: 65  DQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 47.4 bits (113), Expect = 5e-07
 Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            +  E L +   + G V   +   T          + Y  +DQA+ ALD  N   + + 
Sbjct: 25 PHLQWEVLDSLLVQYGVVESCEQVNTDSET--AVVNVTYSSKDQARQALDKLNGFQLENF 82

Query: 87 RIKVE 91
           +KV 
Sbjct: 83 TLKVA 87

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 70.8 bits (174), Expect = 4e-15
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 3/85 (3%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK-ETDKTKGFALVTFLMPEHATQAYQ 396
             F+ NL Y VTE+ + + F      + V LP +    ++ KGF    F   +    A  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 397 HLDGTVFLGRMLHLIPGKPKENEGN 421
            L+      + + +      +++ +
Sbjct: 76  -LNEESLGNKRIRVDVADQAQDKDS 99

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 68.1 bits (167), Expect = 3e-14
 Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 3/95 (3%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
              S + K       + N+P+   +  ++E F+       VRLP++       +GFG+ E
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAE 63

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
           F   +    A+        L  +R+ ++ A++A +
Sbjct: 64  FEDLDSLLSALS--LNEESLGNKRIRVDVADQAQD 96

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 64.6 bits (158), Expect = 7e-13
 Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 7/93 (7%)

Query: 572 DEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
              R P  P  T ++ NL ++ TE+SI+  F+    I++V + R  +P +P +    G+G
Sbjct: 6   SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERLK--GFG 60

Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
           + +F   +SL  AL  L   SL   +I +  ++
Sbjct: 61  YAEFEDLDSLLSALS-LNEESLGNKRIRVDVAD 92

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 13/93 (13%)

Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TT-- 256
             S  S   + K+P +     T  + NLP  V ++ +K +F+ L +++VR          
Sbjct: 1   GSSGSSGSRLPKSPPY-----TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPER 55

Query: 257 FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
             G  Y  F+D  +   AL+ N+     K++ +
Sbjct: 56  LKGFGYAEFEDLDSLLSALSLNEESLGNKRIRV 88

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
          Y +T+E +K  F     ++ V+L  + +   + + F +  +   D   +AL   N   + 
Sbjct: 25 YDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLG 82

Query: 85 SSRIKVE 91
          + RI+V+
Sbjct: 83 NKRIRVD 89

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 71.2 bits (175), Expect = 4e-15
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +FV NL Y V    L ++F   G +    +  DK+  K++G   VTF     A QA   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISM 75

Query: 398 LDGTVFLGRMLHLIPGKPKENEGN 421
            +G +   R +H+   +    +G+
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGD 99

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 63.9 bits (156), Expect = 1e-12
 Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 6/111 (5%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +     +T+++ NL++      ++  F   G +    +   KD    G+  S G G V F
Sbjct: 10  QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD----GK--SRGIGTVTF 63

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
                  QA+ +     L +  + +K   R L         +       +G
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 63.5 bits (155), Expect = 2e-12
 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 3/88 (3%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
           A + GS + V N+ ++    +++E+F   G +    + +     G  RG G V F    E
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED--KDGKSRGIGTVTFEQSIE 68

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEAD 768
           A +A+        L+ R + ++  E A 
Sbjct: 69  AVQAISMF-NGQLLFDRPMHVKMDERAL 95

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 54.2 bits (131), Expect = 3e-09
 Identities = 16/64 (25%), Positives = 28/64 (43%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          YK+  ++LK  F   G V    +    +GK R    + + +  +A  A+  FN   +F  
Sbjct: 25 YKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDR 84

Query: 87 RIKV 90
           + V
Sbjct: 85 PMHV 88

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.8 bits (91), Expect = 7e-04
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 5/59 (8%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 503
           + V NL Y+     LK +F   G + R  +     G     G V F Q  +A  A +  
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 72.2 bits (177), Expect = 5e-15
 Identities = 25/141 (17%), Positives = 49/141 (34%), Gaps = 9/141 (6%)

Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDE--HQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
           G    +     +  +  K   N +  +     +       +   +          +    
Sbjct: 14  GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLD 73

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            K+ V N+     ++E+E  F  +G L+ V + +         GF FVEF    +A  A+
Sbjct: 74  CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN------PPGFAFVEFEDPRDAADAV 127

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
           + L     L G R+ +E +  
Sbjct: 128 REL-DGRTLCGCRVRVELSNG 147

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 71.8 bits (176), Expect = 6e-15
 Identities = 28/115 (24%), Positives = 40/115 (34%), Gaps = 9/115 (7%)

Query: 292 YSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTED 351
           Y+ DN        DD          + H           +      +++V NL     + 
Sbjct: 33  YANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHR----DSCPLDCKVYVGNLGNNGNKT 88

Query: 352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR 406
           +L + F  YGPL  V +  +       GFA V F  P  A  A + LDG    G 
Sbjct: 89  ELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRELDGRTLCGC 138

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 61.0 bits (148), Expect = 4e-11
 Identities = 29/138 (21%), Positives = 50/138 (36%), Gaps = 12/138 (8%)

Query: 528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE--REPEPDTTLYI 585
           E       EK  ++         E T ++  +        +             D  +Y+
Sbjct: 19  EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYV 78

Query: 586 KNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALK 645
            NL  N  +  + R F   GP+ SV VAR  +P         G+ FV+F        A++
Sbjct: 79  GNLGNNGNKTELERAFGYYGPLRSVWVAR--NPP--------GFAFVEFEDPRDAADAVR 128

Query: 646 VLQNSSLDEHQIELKRSN 663
            L   +L   ++ ++ SN
Sbjct: 129 ELDGRTLCGCRVRVELSN 146

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 44.5 bits (105), Expect = 2e-05
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 4/66 (6%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
               + +L+  F   G +  V +     G    FAF+ +     A  A+   +   +   
Sbjct: 83  NNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELDGRTLCGC 138

Query: 87  RIKVEK 92
           R++VE 
Sbjct: 139 RVRVEL 144

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 70.3 bits (173), Expect = 5e-15
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 3/82 (3%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET-DKTKGFALVTFLMPEHATQAYQ 396
             F+ NL Y VTE+ + + F      + V LP +    ++ KGF    F   +    A  
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 397 HLDGTVFLGRMLHLIPGKPKEN 418
            L+      R + +      ++
Sbjct: 80  -LNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 65.0 bits (159), Expect = 4e-13
 Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
               S + K       + N+P+   +  ++E F+       VRLP++       +GFG+ 
Sbjct: 8   HHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYA 66

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
           EF   +    A+        L  RR+ ++ A++A +
Sbjct: 67  EFEDLDSLLSALS--LNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 63.8 bits (156), Expect = 1e-12
 Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 9/91 (9%)

Query: 570 EEDEEREPEPDT---TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
                R   P +   T ++ NL ++ TE+SI+  F+    I++V + R  +P +P +   
Sbjct: 6   HHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERL-- 60

Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
            G+G+ +F   +SL  AL  L   SL   +I
Sbjct: 61  KGFGYAEFEDLDSLLSALS-LNEESLGNRRI 90

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
          Y +T+E +K  F     ++ V+L  + +   + + F +  +   D   +AL   N   + 
Sbjct: 29 YDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLG 86

Query: 85 SSRIKVE 91
          + RI+V+
Sbjct: 87 NRRIRVD 93

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVR------TT--FLGMAYIGFKDEKNCNKALNK 277
           T  + NLP  V ++ +K +F+ L +++VR            G  Y  F+D  +   AL+ 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80

Query: 278 NKSFWKGKQLNI 289
           N+     +++ +
Sbjct: 81  NEESLGNRRIRV 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 69.9 bits (172), Expect = 6e-15
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           + +IFVRNL +  T   L   F + G +      I  E  K+KG  +V F  PE A +A 
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVAERAC 65

Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
           + ++G    GR + +   +   
Sbjct: 66  RMMNGMKLSGREIDVRIDRNAS 87

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 7/89 (7%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
                 ++++NL F+ T   ++  F +CG +    +  +      G+  S G G V+F +
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-----GK--SKGCGVVKFES 57

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRN 665
            E   +A +++    L   +I+++     
Sbjct: 58  PEVAERACRMMNGMKLSGREIDVRIDRNA 86

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 61.1 bits (149), Expect = 9e-12
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 4/88 (4%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
                 +I VRN+PF      +++ F   G + +  +    + +G  +G G V+F +   
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI---KMENGKSKGCGVVKFESPEV 60

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEAD 768
           A+RA + +     L GR + +     A 
Sbjct: 61  AERACRMM-NGMKLSGREIDVRIDRNAS 87

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          +  T + LK KF E G V    +K    GK +    + +   + A+ A    N   +   
Sbjct: 18 FDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACRMMNGMKLSGR 76

Query: 87 RIKV 90
           I V
Sbjct: 77 EIDV 80

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 70.0 bits (172), Expect = 7e-15
 Identities = 19/102 (18%), Positives = 36/102 (35%), Gaps = 9/102 (8%)

Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETD 375
           + H      S           R+F+ NL    V+++DL ++F  YG + ++ +       
Sbjct: 3   SSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------ 56

Query: 376 KTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
               F  + F  P+    A +     +  G+ L L       
Sbjct: 57  --NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 65.0 bits (159), Expect = 3e-13
 Identities = 14/83 (16%), Positives = 37/83 (44%), Gaps = 11/83 (13%)

Query: 685 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
            S++ + N+P +   + ++  +F  +G +  + +            FGF++F      + 
Sbjct: 22  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 72

Query: 744 AMKALCQSTHLYGRRLVLEWAEE 766
           A++        +G++L+LE +  
Sbjct: 73  AIEXE-SQEMNFGKKLILEVSSS 94

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 14/90 (15%)

Query: 575 REPEPDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
           R     + L+I NL   + +++ + R F   G I  + +                +GF+Q
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------------AFGFIQ 63

Query: 634 FYTRESLNQALKVLQNSSLDEHQIELKRSN 663
           F   +S+  A++          ++ L+ S+
Sbjct: 64  FDNPQSVRDAIEXESQEMNFGKKLILEVSS 93

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 7/64 (10%)

Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           +++E L   F   G +  + +K         F FI +      + A++  +    F  +
Sbjct: 34 NVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK 86

Query: 88 IKVE 91
          + +E
Sbjct: 87 LILE 90

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 70.0 bits (172), Expect = 1e-14
 Identities = 20/80 (25%), Positives = 40/80 (50%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +F+ +L     + DL ++F  +G +    + IDK+T+ +K F  V++  P  A  A Q +
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 399 DGTVFLGRMLHLIPGKPKEN 418
           +G     + L +   + K +
Sbjct: 88  NGFQIGMKRLKVQLKRSKND 107

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 16/110 (14%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
           S+ +      ++    S      G+ + + ++P +    ++ ++F  FG +   ++    
Sbjct: 2   SSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKV---F 58

Query: 722 V--GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
           +   + L + FGFV +     A+ A++++     +  +RL ++     ++
Sbjct: 59  IDKQTNLSKCFGFVSYDNPVSAQAAIQSM-NGFQIGMKRLKVQLKRSKND 107

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 54.6 bits (132), Expect = 3e-09
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 10/90 (11%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
             ++E      L+I +L     +  + + F   G + S  V    D ++     S  +GF
Sbjct: 17  GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI--DKQT-NL--SKCFGF 71

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKR 661
           V +    S   A++     S++  QI +KR
Sbjct: 72  VSYDNPVSAQAAIQ-----SMNGFQIGMKR 96

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 5/67 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
           +   + L   F   G V   ++   K T     + F F+ Y     AQAA+   N   +
Sbjct: 35 QEFGDQDLLQMFMPFGNVVSAKVFIDKQT--NLSKCFGFVSYDNPVSAQAAIQSMNGFQI 92

Query: 84 FSSRIKV 90
             R+KV
Sbjct: 93 GMKRLKV 99

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 68.6 bits (168), Expect = 1e-14
 Identities = 20/73 (27%), Positives = 26/73 (35%), Gaps = 7/73 (9%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S  I V+NL       ++  L + Y              D+ K  A VT L  E A  A 
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 396 QHLDGTVFLGRML 408
           Q      F G+ L
Sbjct: 58  QMFHQYSFRGKDL 70

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 67.8 bits (166), Expect = 3e-14
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 9/80 (11%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S ILV+N+P  +   EV +L K +          K      ++   FV  +   +A+ A+
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD--------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 746 KALCQSTHLYGRRLVLEWAE 765
           +   Q     G+ L+++   
Sbjct: 58  QMFHQ-YSFRGKDLIVQLQP 76

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 54.7 bits (132), Expect = 1e-09
 Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 1/76 (1%)

Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 503
           +     ILVKNLP  +   ++  L + +  L    V     T  V  L   QA+ A    
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 504 AYTKFKEVPLYLEWAP 519
               F+   L ++  P
Sbjct: 61  HQYSFRGKDLIVQLQP 76

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 12/82 (14%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           + + +KNL  +S    +    K    +    V R K              FV     E  
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK-----------RTAFVTLLNGEQA 53

Query: 641 NQALKVLQNSSLDEHQIELKRS 662
             A+++    S     + ++  
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQ 75

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 43.6 bits (103), Expect = 9e-06
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL-GMAYIGFKDEKNCNKALNK-NKSFWK 283
            I+VKNLP     +++    K   L           A++   + +    A+   ++  ++
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFR 66

Query: 284 GKQLNIYKYSKDNSAKYSG 302
           GK L + +    ++   SG
Sbjct: 67  GKDLIV-QLQPTDALLCSG 84

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 6/65 (9%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
               +++    ++        LKY    + +R AF+     +QAQ A+  F+       
Sbjct: 15 QDSNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGK 68

Query: 87 RIKVE 91
           + V+
Sbjct: 69 DLIVQ 73

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 69.4 bits (170), Expect = 2e-14
 Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 1/85 (1%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
                 + N+ +++T+ D+ +  E        +  +     +  G ALV F   + A ++
Sbjct: 14  AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 73

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENE 419
            + L      GR   +     ++  
Sbjct: 74  -ERLHRKKLNGREAFVHVVTLEDMR 97

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 64.8 bits (158), Expect = 6e-13
 Identities = 16/107 (14%), Positives = 35/107 (32%), Gaps = 5/107 (4%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGF 732
                           + NIPF   + +V +  +     +  V +      +G   G   
Sbjct: 4   GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--NNGQGLGQAL 61

Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
           V+F  +++A+++ +       L GR   +      D  E  +    +
Sbjct: 62  VQFKNEDDARKSER--LHRKKLNGREAFVHVVTLEDMREIEKNPPAQ 106

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 62.1 bits (151), Expect = 6e-12
 Identities = 13/94 (13%), Positives = 31/94 (32%), Gaps = 8/94 (8%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMGYGF 631
           E          +I N+ F+ T+  + +  +       +V V    + +       +G   
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ------GLGQAL 61

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
           VQF   +   ++ + L    L+  +  +      
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFVHVVTLE 94

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.2 bits (141), Expect = 2e-10
 Identities = 14/108 (12%), Positives = 37/108 (34%), Gaps = 8/108 (7%)

Query: 212 PPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYI 263
              S             + N+P  + K D+  + + +P+       L        G A +
Sbjct: 3   SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALV 62

Query: 264 GFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNAS 311
            FK+E +  K+   ++    G++  ++  + ++  +          + 
Sbjct: 63  QFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 110

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.5 bits (108), Expect = 3e-06
 Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 7/91 (7%)

Query: 27  YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD----YFNNT 81
           + IT+  +    E      + V +     G+    A + +  ED A+ +        N  
Sbjct: 25  FSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGR 84

Query: 82  YVFSSRIKVEKCSNLGDTTKPKSWSKYAPDS 112
             F   + +E    +     P +  K  P S
Sbjct: 85  EAFVHVVTLEDMREIEK--NPPAQGKSGPSS 113

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.7 bits (93), Expect = 4e-04
 Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 6/61 (9%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKA 498
            +K    + N+P+     D+    E        +       G      LV+F  ++ A+ 
Sbjct: 13  SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 72

Query: 499 A 499
           +
Sbjct: 73  S 73

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 69.5 bits (170), Expect = 2e-14
 Identities = 23/107 (21%), Positives = 44/107 (41%), Gaps = 5/107 (4%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGF 732
           KR  S    + G  + ++ +PF+A+   V + FK    ++  + +     G     G GF
Sbjct: 14  KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK--ATGEGF 71

Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
           VEF  + + K A+       ++  R + +    +   +E I     R
Sbjct: 72  VEFRNEADYKAALC--RHKQYMGNRFIQVHPITKKGMLEKIDMIRKR 116

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 69.5 bits (170), Expect = 2e-14
 Identities = 13/89 (14%), Positives = 25/89 (28%), Gaps = 1/89 (1%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
               ++++ L +      +   F+K   + + I        K  G   V F        A
Sbjct: 24  AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVD 423
                      R + + P   K     +D
Sbjct: 84  LC-RHKQYMGNRFIQVHPITKKGMLEKID 111

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 66.0 bits (161), Expect = 4e-13
 Identities = 24/119 (20%), Positives = 41/119 (34%), Gaps = 9/119 (7%)

Query: 563 PEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKS 620
            +     +    R P E    +Y+K L F +    +   FKK   +  S+ +A   + K 
Sbjct: 7   GKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK- 65

Query: 621 PGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN 679
                + G GFV+F        AL       +    I++    +    E   + RK   
Sbjct: 66  -----ATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQ 118

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 59.9 bits (145), Expect = 5e-11
 Identities = 18/104 (17%), Positives = 41/104 (39%), Gaps = 8/104 (7%)

Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL-- 258
           S  ++   PS    S++         + +K LP   + K +  +FK L +          
Sbjct: 2   SSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG 61

Query: 259 ------GMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDN 296
                 G  ++ F++E +   AL ++K +   + + ++  +K  
Sbjct: 62  PNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKG 105

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 45.2 bits (107), Expect = 6e-06
 Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 5/90 (5%)

Query: 27  YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           ++   + +   F++   V D + + Y   GK     F+ +  E   +AAL   +  Y+ +
Sbjct: 35  FEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR-HKQYMGN 93

Query: 86  SRIKVEKCSN---LGDTTKPKSWSKYAPDS 112
             I+V   +    L      +   +  P S
Sbjct: 94  RFIQVHPITKKGMLEKIDMIRKRLQSGPSS 123

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 69.0 bits (169), Expect = 2e-14
 Identities = 16/95 (16%), Positives = 34/95 (35%), Gaps = 1/95 (1%)

Query: 323 QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFAL 382
              S   + D A  G + +R L +  +++++ + F     +   +        ++ G A 
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 383 VTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
           V F   E A +A +         R + +      E
Sbjct: 62  VQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAE 95

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 62.8 bits (153), Expect = 2e-12
 Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 8/96 (8%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMG 628
                 +   D  + ++ L F  +++ I + F     +   +T+      +      S G
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR------STG 58

Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
             FVQF ++E   +ALK      +    IE+ +S+R
Sbjct: 59  EAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSR 93

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 57.4 bits (139), Expect = 2e-10
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 674 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFG 731
              S N         + +R +PF   + E+ + F     +   + LP    G     G  
Sbjct: 3   SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR--STGEA 60

Query: 732 FVEFITKNEAKRAMK 746
           FV+F ++  A++A+K
Sbjct: 61  FVQFASQEIAEKALK 75

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 11/94 (11%)

Query: 220 HKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNC 271
                  + ++ LP G  K+++  +F  L +     T          G A++ F  ++  
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

Query: 272 NKALNKNKSFWKGKQLNIYKYSKD---NSAKYSG 302
            KAL K+K     + + I+K S+     S   SG
Sbjct: 71  EKALKKHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          +  ++E++   F     V + + L    +G+    AF+ +  ++ A+ AL   +   +  
Sbjct: 25 FGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGH 83

Query: 86 SRIKVEKCS 94
            I++ K S
Sbjct: 84 RYIEIFKSS 92

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 68.6 bits (168), Expect = 3e-14
 Identities = 20/70 (28%), Positives = 35/70 (50%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +F+ +L    T+ DL   F  +G +    + IDK+T  +K F  V+F  P+ A  A + +
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 399 DGTVFLGRML 408
           +G     + L
Sbjct: 103 NGFQVGTKRL 112

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 57.0 bits (138), Expect = 4e-10
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           ++ E      L+I +L    T+  +   F   G + S  V    D ++     S  +GFV
Sbjct: 33  KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI--DKQT-SL--SKCFGFV 87

Query: 633 QFYTRESLNQALKVLQNSSLDEHQI 657
            F   +S   A+K +    +   ++
Sbjct: 88  SFDNPDSAQVAIKAMNGFQVGTKRL 112

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 56.6 bits (137), Expect = 6e-10
 Identities = 17/92 (18%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFV 733
               +    G  + + ++P +   +++   F  FG +   ++    +   + L + FGFV
Sbjct: 31  AGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKV---FIDKQTSLSKCFGFV 87

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
            F   + A+ A+KA+     +  +RL ++  +
Sbjct: 88  SFDNPDSAQVAIKAM-NGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
            + T   L + F   G V   ++   K T     + F F+ +   D AQ A+   N   V
Sbjct: 50  QEFTDTDLASTFLPFGNVISAKVFIDKQT--SLSKCFGFVSFDNPDSAQVAIKAMNGFQV 107

Query: 84  FSSRIKV 90
            + R+KV
Sbjct: 108 GTKRLKV 114

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 68.6 bits (168), Expect = 3e-14
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 336 SGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           + R+F+ NL+   V + D+  +F KYG +A   +         KG+A V +    HA  A
Sbjct: 27  NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAA 78

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENE 419
               +G V  G+ L +      + +
Sbjct: 79  VLGENGRVLAGQTLDINMAGEPKPD 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 67.8 bits (166), Expect = 6e-14
 Identities = 26/121 (21%), Positives = 51/121 (42%), Gaps = 21/121 (17%)

Query: 668 SEATTVKRKSSNVAKQT-----GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKM 721
           S   ++K ++SNV  +       S++ + N+     K+S+VE +F  +G +    +    
Sbjct: 5   SSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---- 60

Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
                H+G+ FV++  +  A+ A+        L G+ L +  A E         R+    
Sbjct: 61  -----HKGYAFVQYSNERHARAAVLGE-NGRVLAGQTLDINMAGEPK-----PDRSGPSS 109

Query: 782 G 782
           G
Sbjct: 110 G 110

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 57.0 bits (138), Expect = 3e-10
 Identities = 18/110 (16%), Positives = 36/110 (32%), Gaps = 17/110 (15%)

Query: 560 QGVPEVEENVEEDEEREPEPD-TTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKD 617
            G+    +      + +P+   + ++I NLN     +  +   F K G +A  +V +   
Sbjct: 6   SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--- 62

Query: 618 PKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI--ELKRSNRN 665
                     GY FVQ+        A+       L    +   +    + 
Sbjct: 63  ----------GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 7/64 (10%)

Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
           + +  ++  F + G V    +        + +AF+ Y  E  A+AA+   N   +    
Sbjct: 39 LVKKSDVETIFSKYGRVAGCSVH-------KGYAFVQYSNERHARAAVLGENGRVLAGQT 91

Query: 88 IKVE 91
          + + 
Sbjct: 92 LDIN 95

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 67.6 bits (166), Expect = 4e-14
 Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 13/95 (13%)

Query: 332 DIAESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           +I    R+F+ NL    V+++DL ++F  YG + ++ +           F  + F  P+ 
Sbjct: 6   NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQS 57

Query: 391 ATQAYQHLDGTVFLGRMLHL----IPGKPKENEGN 421
              A +     +  G+ L L       +P+ + G+
Sbjct: 58  VRDAIECESQEMNFGKKLILEVSSSNARPQFDHGD 92

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 66.5 bits (163), Expect = 1e-13
 Identities = 16/99 (16%), Positives = 39/99 (39%), Gaps = 18/99 (18%)

Query: 685 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
            S++ + N+P +   + ++  +F  +G +  + +            FGF++F      + 
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 60

Query: 744 AMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
           A++        +G++L+LE +           R     G
Sbjct: 61  AIECE-SQEMNFGKKLILEVSSS-------NARPQFDHG 91

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 14/88 (15%)

Query: 579 PDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           P + L+I NL   + +++ + R F   G I  + +                +GF+QF   
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------------AFGFIQFDNP 55

Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRN 665
           +S+  A++          ++ L+ S+ N
Sbjct: 56  QSVRDAIECESQEMNFGKKLILEVSSSN 83

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 46.8 bits (112), Expect = 8e-07
 Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 7/65 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            +++E L   F   G +  + +K         F FI +      + A++  +    F  
Sbjct: 21 KNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGK 73

Query: 87 RIKVE 91
          ++ +E
Sbjct: 74 KLILE 78

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 67.1 bits (164), Expect = 5e-14
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-----IDKETDKTKGFALVTFLMPEHAT 392
           R++V N+ + +TE+ +   F     L  +        +  + ++ K FA + F   +  T
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 393 QAYQHLDGTVFLGRML 408
           QA    DG +F G+ L
Sbjct: 68  QAMA-FDGIIFQGQSL 82

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 742
           ++ V NIPF   +  + + F A   L  +      P   V     + F F+EF + +E  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 743 RAMKALCQSTHLYGRRL 759
           +AM A        G+ L
Sbjct: 68  QAM-AF-DGIIFQGQSL 82

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LY+ N+ F  TE+++   F     +  +T A      +        + F++F + +   Q
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 643 ALKVLQNSSLDEHQIELKR 661
           A+            ++++R
Sbjct: 69  AMA-FDGIIFQGQSLKIRR 86

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 67.3 bits (165), Expect = 7e-14
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R++V  L    +   L + F+++G +  +             FA + +   + A  A   
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 398 LDGTVFLG 405
           + G    G
Sbjct: 73  MRGFPLGG 80

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 64.6 bits (158), Expect = 4e-13
 Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 11/77 (14%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
             P T L++  L  N++  ++ R F + G I ++   +              + ++Q+ +
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-----------SFAYIQYES 62

Query: 637 RESLNQALKVLQNSSLD 653
            ++   A   ++   L 
Sbjct: 63  LDAAQAACAKMRGFPLG 79

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 10/77 (12%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
           V  +      + +   F  FG ++ +   K          F ++++ + + A+ A   + 
Sbjct: 22  VGGLGPNTSLAALAREFDRFGSIRTIDHVK-------GDSFAYIQYESLDAAQAACAKM- 73

Query: 750 QSTHLYG--RRLVLEWA 764
           +   L G  RRL +++A
Sbjct: 74  RGFPLGGPDRRLRVDFA 90

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 10/52 (19%), Positives = 19/52 (36%)

Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 503
           V  L   T    L   F+ FG +  +          +++   + A+AA   +
Sbjct: 22  VGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKM 73

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 7/67 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             +   L  +F+  G++  +        K   FA+I Y   D AQAA        +   
Sbjct: 27 PNTSLAALAREFDRFGSIRTIDHV-----KGDSFAYIQYESLDAAQAACAKMRGFPLGGP 81

Query: 87 --RIKVE 91
            R++V+
Sbjct: 82 DRRLRVD 88

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 66.9 bits (164), Expect = 8e-14
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           E       +FV  +   + E ++   F +YG + EV +  D+ T  +KG+  V+F     
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD 62

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
             +  +      F G+ L L P   K+N
Sbjct: 63  VQKIVE--SQINFHGKKLKLGPAIRKQN 88

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 18/91 (19%), Positives = 36/91 (39%), Gaps = 10/91 (10%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
            T+++  ++    E  IR  F + G +  V +   +         S GYGFV FY     
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV------SKGYGFVSFYNDVD- 62

Query: 641 NQALKVLQNS-SLDEHQIELKRSNRNLESEA 670
               K++++  +    +++L  + R      
Sbjct: 63  --VQKIVESQINFHGKKLKLGPAIRKQNLST 91

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 52.6 bits (127), Expect = 8e-09
 Identities = 19/96 (19%), Positives = 44/96 (45%), Gaps = 5/96 (5%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
            K   + + V  I  +  ++E+   F  +G +K V++      +G+ +G+GFV F    +
Sbjct: 5   GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVD 62

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKR 776
            ++ ++      + +G++L L  A    N+     +
Sbjct: 63  VQKIVE---SQINFHGKKLKLGPAIRKQNLSTYHVQ 95

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 7/50 (14%), Positives = 26/50 (52%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
           ++ + ++++ F   G+V +V++     G  + + F+ ++ +   Q  ++
Sbjct: 19 VRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 68.3 bits (167), Expect = 9e-14
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPL----AEVILPI-DKETDKTKGFALVTFLMPEH 390
           + RI+V+NL+  V E DL  +F +Y         ++  I   +  + KG A +     + 
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           A +A +  +G V  G+ + +   +    
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSARP 132

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 62.5 bits (152), Expect = 9e-12
 Identities = 22/133 (16%), Positives = 47/133 (35%), Gaps = 1/133 (0%)

Query: 539 EEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSI 597
                +    +  +  E +  +   E  E +      EP EP+  +Y+KNL  +  E  +
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62

Query: 598 RRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
           +  F +    +S T     D +   +    G  F+     ++  +ALK      L    +
Sbjct: 63  KYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM 122

Query: 658 ELKRSNRNLESEA 670
            ++ +      + 
Sbjct: 123 VVQFARSARPKQD 135

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 56.4 bits (136), Expect = 1e-09
 Identities = 19/139 (13%), Positives = 56/139 (40%), Gaps = 8/139 (5%)

Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
                 + +  +   ++E  R +R      +  +             I V+N+    ++ 
Sbjct: 4   GSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCR---IYVKNLAKHVQEK 60

Query: 701 EVEELFKAFGEL----KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
           +++ +F  + +     + +    +++  G  +G  F+    +  A +A+K       L+G
Sbjct: 61  DLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEA-NGYVLFG 119

Query: 757 RRLVLEWAEEADNVEDIRK 775
           + +V+++A  A   +D ++
Sbjct: 120 KPMVVQFARSARPKQDPKE 138

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 41.0 bits (96), Expect = 3e-04
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 6/71 (8%)

Query: 27  YKITQEQLKAKFEEKGTVTD------VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
             + ++ LK  F      +         ++   EG+ +  AFIG   E  A  AL   N 
Sbjct: 55  KHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANG 114

Query: 81  TYVFSSRIKVE 91
             +F   + V+
Sbjct: 115 YVLFGKPMVVQ 125

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 39.4 bits (92), Expect = 8e-04
 Identities = 20/116 (17%), Positives = 32/116 (27%), Gaps = 13/116 (11%)

Query: 431 SERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGIT---- 485
               L  F           I VKNL       DLK +F  + D         + I     
Sbjct: 29  EMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE 88

Query: 486 ------GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 535
                   +    +  A  A            P+ +++A        ++  +GK K
Sbjct: 89  GRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA--RPKQDPKEGKRK 142

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 66.4 bits (163), Expect = 1e-13
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           ++S +IFV  + +   E +L + F+K+G + EV++  D E  + +GF  +TF   +   Q
Sbjct: 8   SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQ 67

Query: 394 A----YQHLDG 400
           A    +  + G
Sbjct: 68  AVNMHFHDIMG 78

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 6/86 (6%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
                  +++  +  N  E  +R +FKK G +  V +    D +   +    G+GF+ F 
Sbjct: 6   SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVM--IYDAEK-QR--PRGFGFITFE 60

Query: 636 TRESLNQALKVLQNSSLDEHQIELKR 661
             +S++QA+  +    +   ++E+KR
Sbjct: 61  DEQSVDQAVN-MHFHDIMGKKVEVKR 85

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 47.2 bits (113), Expect = 7e-07
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
           SS  +    +KI V  IP    ++E+ E FK FG +  V +          RGFGF+ F 
Sbjct: 2   SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA-EKQRPRGFGFITFE 60

Query: 737 TKNEAKRAMKA 747
            +    +A+  
Sbjct: 61  DEQSVDQAVNM 71

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVI-LPIDKETDKTKGFALVTFLMPEHATQA 394
           S  IF+ NL   + E  L   F  +G + +   +  D +T  +KG+A + F   + +  A
Sbjct: 5   SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
            + ++G     R + +     K+++G+
Sbjct: 65  IEAMNGQYLCNRPITVSYAFKKDSKGS 91

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT-VARKKDPKSPGQFLSMGYGFVQFYTR 637
             + ++I NL+    E  +   F   G I     + R  DP + G   S GY F+ F + 
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR--DPDT-GN--SKGYAFINFASF 58

Query: 638 ESLNQALKVLQNSSLDEHQI 657
           ++ + A++ +    L    I
Sbjct: 59  DASDAAIEAMNGQYLCNRPI 78

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 20/86 (23%), Positives = 45/86 (52%), Gaps = 5/86 (5%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 743
           S I + N+  +  +  + + F AFG +  ++ PK M    +G  +G+ F+ F + + +  
Sbjct: 6   SGIFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 744 AMKALCQSTHLYGRRLVLEWAEEADN 769
           A++A+    +L  R + + +A + D+
Sbjct: 64  AIEAM-NGQYLCNRPITVSYAFKKDS 88

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 67.2 bits (164), Expect = 1e-13
 Identities = 19/112 (16%), Positives = 42/112 (37%), Gaps = 8/112 (7%)

Query: 554 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTV 612
               +   +   ++        +   D  + ++ L F  T++ I + F     +   +T+
Sbjct: 16  PRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75

Query: 613 ARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
               + K        G  FVQF ++E   +AL       +    IE+ +S++
Sbjct: 76  PVDPEGK------ITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQ 120

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 66.4 bits (162), Expect = 2e-13
 Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 1/96 (1%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
            Q      + D A  G + +R L +  T++++ + F     +   I        K  G A
Sbjct: 28  QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87

Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
            V F   E A +A           R + +     +E
Sbjct: 88  FVQFASQELAEKALG-KHKERIGHRYIEVFKSSQEE 122

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 59.5 bits (144), Expect = 7e-11
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 3/86 (3%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKK 720
           S+    +    + R S++        + +R +PF   + E+ + F     +   + LP  
Sbjct: 19  SHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVD 78

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMK 746
             G     G  FV+F ++  A++A+ 
Sbjct: 79  PEGK--ITGEAFVQFASQELAEKALG 102

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 51.8 bits (124), Expect = 3e-08
 Identities = 18/105 (17%), Positives = 39/105 (37%), Gaps = 8/105 (7%)

Query: 199 TKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL 258
             S   + +                   + ++ LP G  K+++  +F  L +     T  
Sbjct: 17  RGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLP 76

Query: 259 --------GMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKD 295
                   G A++ F  ++   KAL K+K     + + ++K S++
Sbjct: 77  VDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQE 121

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 43.7 bits (103), Expect = 2e-05
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 27  YKITQEQLKAKFEEKGTV-TDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
           +  T+E++   F     V   + L    EGK    AF+ +  ++ A+ AL   +   +  
Sbjct: 52  FGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGH 110

Query: 86  SRIKVEKCS 94
             I+V K S
Sbjct: 111 RYIEVFKSS 119

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 72.6 bits (177), Expect = 2e-13
 Identities = 28/140 (20%), Positives = 56/140 (40%), Gaps = 10/140 (7%)

Query: 533 KEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVE-----EDEEREPEPDTTLYIKN 587
             ++       E  EE+ E    E  ++   EVE  ++      D   + +   TL++  
Sbjct: 50  DPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVAR 109

Query: 588 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
           +N+++TE  +RR F+  GPI  + +   K    P      GY F+++     ++ A K  
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKP-----RGYAFIEYEHERDMHSAYKHA 164

Query: 648 QNSSLDEHQIELKRSNRNLE 667
               +D  ++ +        
Sbjct: 165 DGKKIDGRRVLVDVERGRTV 184

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 64.9 bits (157), Expect = 4e-11
 Identities = 22/73 (30%), Positives = 37/73 (50%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +FV  ++Y  TE  L + FE YGP+  + +   K + K +G+A + +        AY+H 
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 399 DGTVFLGRMLHLI 411
           DG    GR + + 
Sbjct: 165 DGKKIDGRRVLVD 177

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 41.8 bits (97), Expect = 8e-04
 Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V  + +   +S++   F+ +G +K + +      SG  RG+ F+E+  + +   A K 
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVY-SKRSGKPRGYAFIEYEHERDMHSAYKH 163

Query: 748 LCQSTHLYGRRLVLEWAEE 766
                 + GRR++++    
Sbjct: 164 A-DGKKIDGRRVLVDVERG 181

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 11/74 (14%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           TTLY+  L    TE  +R HF + G I ++TV +++              F+QF TR++ 
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-----------QCAFIQFATRQAA 61

Query: 641 NQALKVLQNSSLDE 654
             A +   N  +  
Sbjct: 62  EVAAEKSFNKLIVN 75

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 61.5 bits (150), Expect = 4e-12
 Identities = 15/75 (20%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
           V  +     ++++   F  FGE++ + + ++       +   F++F T+  A+ A +   
Sbjct: 17  VGGLGDTITETDLRNHFYQFGEIRTITVVQR-------QQCAFIQFATRQAAEVAAEKSF 69

Query: 750 QSTHLYGRRLVLEWA 764
               + GRRL ++W 
Sbjct: 70  NKLIVNGRRLNVKWG 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH- 397
           ++V  L  T+TE DL   F ++G +  + +         +  A + F   + A  A +  
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 398 LDGTVFLGRMLHL 410
            +  +  GR L++
Sbjct: 69  FNKLIVNGRRLNV 81

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQA-KAAFNSL 503
           ++   + V  L      TDL+  F  FG++  + V        ++F  +  A  AA  S 
Sbjct: 10  KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSF 69

Query: 504 AYTKFKEVPLYLEWA 518
                    L ++W 
Sbjct: 70  NKLIVNGRRLNVKWG 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 6/65 (9%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGY-HREDQAQAALDYFNNTYVFS 85
            IT+  L+  F + G +  + +        ++ AFI +  R+    AA   FN   V  
Sbjct: 22 DTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNG 76

Query: 86 SRIKV 90
           R+ V
Sbjct: 77 RRLNV 81

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 6/85 (7%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHAT 392
           +   ++V+NL   + ++ L K F  +G +  A+V+     E  ++KGF  V F  PE AT
Sbjct: 14  QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM----MEGGRSKGFGFVCFSSPEEAT 69

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKE 417
           +A   ++G +   + L++   + KE
Sbjct: 70  KAVTEMNGRIVATKPLYVALAQRKE 94

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 4/93 (4%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
                 + +     + V+N+        + + F  FG +   ++   M+  G  +GFGFV
Sbjct: 4   GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV---MMEGGRSKGFGFV 60

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
            F +  EA +A+  +     +  + L +  A+ 
Sbjct: 61  CFSSPEEATKAVTEM-NGRIVATKPLYVALAQR 92

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 54.5 bits (132), Expect = 2e-09
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 7/85 (8%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           +         LY+KNL+    ++ +R+ F   G I S  V  +      G+  S G+GFV
Sbjct: 8   DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-----GR--SKGFGFV 60

Query: 633 QFYTRESLNQALKVLQNSSLDEHQI 657
            F + E   +A+  +    +    +
Sbjct: 61  CFSSPEEATKAVTEMNGRIVATKPL 85

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            I  E+L+  F   GT+T  ++     G+ + F F+ +   ++A  A+   N   V + 
Sbjct: 25 DGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 83

Query: 87 RIKV 90
           + V
Sbjct: 84 PLYV 87

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 65.8 bits (161), Expect = 3e-13
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
           S    +  ++      +IFV  L Y  T+  L K FE +G + E ++  D++T K++G+ 
Sbjct: 3   SGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG 62

Query: 382 LVTFLMPEHATQA----YQHLDG 400
            VT      A +A       +DG
Sbjct: 63  FVTMADRAAAERACKDPNPIIDG 85

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 57.7 bits (140), Expect = 2e-10
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 6/87 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           ++    T +++  L +++T+ S+R++F+  G I    V    D ++ G+  S GYGFV  
Sbjct: 12  QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV--ITDRQT-GK--SRGYGFVTM 66

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKR 661
             R +  +A K   N  +D  +  +  
Sbjct: 67  ADRAAAERACKDP-NPIIDGRKANVNL 92

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.1 bits (102), Expect = 3e-05
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 743
           +KI V  +P+    + + + F+ FG+++   +   +    +G  RG+GFV    +  A+R
Sbjct: 18  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV---ITDRQTGKSRGYGFVTMADRAAAER 74

Query: 744 AMKA 747
           A K 
Sbjct: 75  ACKD 78

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 66.5 bits (162), Expect = 3e-13
 Identities = 17/101 (16%), Positives = 35/101 (34%), Gaps = 7/101 (6%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKT 377
              D          S  + + N++  V ++ L      L    G + ++++     +D  
Sbjct: 15  DSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDN 71

Query: 378 KGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            G A + F   E A    +   G  F G  L +   +  ++
Sbjct: 72  SGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 58.0 bits (140), Expect = 3e-10
 Identities = 23/138 (16%), Positives = 44/138 (31%), Gaps = 26/138 (18%)

Query: 550 KENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH----FKKCG 605
           KE  A +  +Q +   +           EP   + I N+N    ++ ++          G
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPH---TEPSQVVLITNINPEVPKEKLQALLYALASSQG 58

Query: 606 PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
            I  + V    D          G  ++ F T+ES    ++  Q      + + +  S   
Sbjct: 59  DILDIVVDLSDDNS--------GKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS--- 107

Query: 666 LESEATTVKRKSSNVAKQ 683
                   +   S VA+ 
Sbjct: 108 --------ETPQSQVAED 117

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 57.6 bits (139), Expect = 3e-10
 Identities = 17/115 (14%), Positives = 44/115 (38%), Gaps = 9/115 (7%)

Query: 660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE----VEELFKAFGELKFV 715
             + +       +    S+    +    +L+ NI  +  + +    +  L  + G++  +
Sbjct: 4   TAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDI 63

Query: 716 RLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNV 770
            +      S  + G  ++ F T+  A+  ++A  Q     G  LV+ ++E   + 
Sbjct: 64  VVDL----SDDNSGKAYIVFATQESAQAFVEAF-QGYPFQGNPLVITFSETPQSQ 113

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 48.0 bits (114), Expect = 8e-07
 Identities = 16/119 (13%), Positives = 38/119 (31%), Gaps = 15/119 (12%)

Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLV---PPYGIT 485
              D  +        +++L+ N+        L+    AL    GD+  ++V         
Sbjct: 15  DSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGK 74

Query: 486 GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEE 544
             + F  +  A+A   +     F+  PL + +        ++       ++ + E    
Sbjct: 75  AYIVFATQESAQAFVEAFQGYPFQGNPLVITF--------SETPQSQVAEDGSLEHHHH 125

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 42.6 bits (100), Expect = 5e-05
 Identities = 11/69 (15%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 27  YKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
            ++ +E+L+    A    +G + D+ +  +        A+I +  ++ AQA ++ F    
Sbjct: 39  PEVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQAFVEAFQGYP 96

Query: 83  VFSSRIKVE 91
              + + + 
Sbjct: 97  FQGNPLVIT 105

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 65.1 bits (159), Expect = 4e-13
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
              S+    TG  + +R +P++A ++++   F     ++ V +       G   G   VE
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGP--DGRVTGEADVE 61

Query: 735 FITKNEAKRAMK 746
           F T  +A  AM 
Sbjct: 62  FATHEDAVAAMA 73

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 61.3 bits (149), Expect = 9e-12
 Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 8/95 (8%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
                 +      ++++ L + +TE+ I   F    P+  V +    D +        G 
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGR------VTGE 57

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
             V+F T E    A+     +++    +EL  ++ 
Sbjct: 58  ADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST 91

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 59.3 bits (144), Expect = 4e-11
 Identities = 21/82 (25%), Positives = 29/82 (35%), Gaps = 3/82 (3%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + +R L Y  TE+D+   F    P   V + I  +  +  G A V F   E A  A    
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDG-RVTGEADVEFATHEDAVAAMA-K 74

Query: 399 DGTVFLGRMLHLIPGKPKENEG 420
           D      R + L         G
Sbjct: 75  DKANMQHRYVELFLNSTAGTSG 96

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 9/97 (9%)

Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TTFLGMAYIGFKDE 268
           S +       H + ++ LP    + D+  +F PL    V           G A + F   
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATH 65

Query: 269 KNCNKALNKNKSFWKGKQLNIYKYSK---DNSAKYSG 302
           ++   A+ K+K+  + + + ++  S      S   SG
Sbjct: 66  EDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSSG 102

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 10/69 (14%), Positives = 26/69 (37%), Gaps = 2/69 (2%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          Y+ T+  +   F        V ++   +G+    A + +   + A AA+   +   +   
Sbjct: 25 YRATENDIYNFFSP-LNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHR 82

Query: 87 RIKVEKCSN 95
           +++   S 
Sbjct: 83 YVELFLNST 91

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 64.5 bits (157), Expect = 5e-13
 Identities = 15/90 (16%), Positives = 30/90 (33%), Gaps = 5/90 (5%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
            E    +  ++V NL       DL +   + G +     P+       +  A + +    
Sbjct: 13  GEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSA 67

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            A QA   L G       L +   + + ++
Sbjct: 68  AAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 60.6 bits (147), Expect = 1e-11
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
             + + V N+P  A+ S+++   +  G +     P ++   G  R   F+ +     A++
Sbjct: 18  LAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQG-PRRRAFLHYPDSAAAQQ 71

Query: 744 AMKALCQSTHLYGRRLVLEWAEEADN 769
           A+  L Q   L    L +  A +  +
Sbjct: 72  AVSCL-QGLRLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 54.1 bits (130), Expect = 3e-09
 Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 12/95 (12%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
                     +Y+ NL  ++    ++R  ++ G +      +   P+           F+
Sbjct: 12  PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG--PR--------RRAFL 61

Query: 633 QFYTRESLNQALKVLQNSSLDEHQI--ELKRSNRN 665
            +    +  QA+  LQ   L    +   L R  R+
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 38.3 bits (89), Expect = 9e-04
 Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 8/89 (8%)

Query: 203 DTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL---G 259
            +  S P  PP   AP        + V NLP   +  DLK   + L    +R T+     
Sbjct: 2   SSGSSGPGSPPGEGAP----LAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR 57

Query: 260 MAYIGFKDEKNCNKALNK-NKSFWKGKQL 287
            A++ + D     +A++           L
Sbjct: 58  RAFLHYPDSAAAQQAVSCLQGLRLGTDTL 86

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 63.9 bits (156), Expect = 7e-13
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 3/82 (3%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + +R   + VTE ++ +      P   + +  +       G+  V F   E   QA +  
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLKP-VAIRIVRNAHG-NKTGYIFVDFSNEEEVKQALK-C 69

Query: 399 DGTVFLGRMLHLIPGKPKENEG 420
           +     GR + +   K   + G
Sbjct: 70  NREYMGGRYIEVFREKSGPSSG 91

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 63.5 bits (155), Expect = 1e-12
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
           SS  +  T   + +R  PF   +  V E       +  +R+ +   G+    G+ FV+F 
Sbjct: 2   SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNAHGN--KTGYIFVDFS 58

Query: 737 TKNEAKRAMK 746
            + E K+A+K
Sbjct: 59  NEEEVKQALK 68

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 63.1 bits (154), Expect = 2e-12
 Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 8/89 (8%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
                 T+ ++   FN TE ++        P+ ++ + R             GY FV F 
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGN------KTGYIFVDFS 58

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNR 664
             E + QALK      +    IE+ R   
Sbjct: 59  NEEEVKQALK-CNREYMGGRYIEVFREKS 86

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 9/84 (10%)

Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TTFLGMAYIGFKDEKNCNKALNKN 278
           HT+ ++  P  V +K++  +  PL   ++R          G  ++ F +E+   +AL  N
Sbjct: 11  HTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCN 70

Query: 279 KSFWKGKQLNIYKYSKDNSAKYSG 302
           + +  G+ + ++   ++ S   SG
Sbjct: 71  REYMGGRYIEVF---REKSGPSSG 91

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 10/69 (14%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          + +T++ +            +++     G    + F+ +  E++ + AL   N  Y+   
Sbjct: 20 FNVTEKNVMEFLAP-LKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGR 77

Query: 87 RIKVEKCSN 95
           I+V +  +
Sbjct: 78 YIEVFREKS 86

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 64.5 bits (157), Expect = 9e-13
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 339 IFVRNLSYTVTEDDLTK---LFEKYGPLAEVILPIDKETDKTK---GFALVTFLMPEHAT 392
           +FV  LS  + + ++ K    F K+G + +V++        ++     A VT++  E A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 393 QAYQHLDGTVFLGRML 408
           +A Q ++  V  GR L
Sbjct: 78  RAIQCVNNVVVDGRTL 93

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 53.7 bits (129), Expect = 6e-09
 Identities = 11/79 (13%), Positives = 28/79 (35%), Gaps = 5/79 (6%)

Query: 582 TLYIKNLNFNSTEDSIRR---HFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
            +++  L+    +  + +   +F K G I  V +                  +V +   E
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQG--PSASAYVTYIRSE 74

Query: 639 SLNQALKVLQNSSLDEHQI 657
              +A++ + N  +D   +
Sbjct: 75  DALRAIQCVNNVVVDGRTL 93

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 690 VRNIPFQAKQSEV---EELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRA 744
           V  +  +    EV    E F  FG++  V +       GS       +V +I   +A RA
Sbjct: 20  VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79

Query: 745 MKALCQSTHLYGRRLVLEWA 764
           ++ +  +  + GR L     
Sbjct: 80  IQCV-NNVVVDGRTLKASLG 98

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 41.8 bits (98), Expect = 7e-05
 Identities = 26/111 (23%), Positives = 46/111 (41%), Gaps = 19/111 (17%)

Query: 9   VVPRNHISLLDLDEVEFIYKITQEQL---KAKFEEKGTVTDVQLKYTTEGKFRR----FA 61
           VV +N + ++ L       ++   ++      F + G +  V +  +T     +     A
Sbjct: 12  VVQKNLVFVVGLS-----QRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASA 66

Query: 62  FIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDS 112
           ++ Y R + A  A+   NN  V    +K     +LG TTK  S+S   P S
Sbjct: 67  YVTYIRSEDALRAIQCVNNVVVDGRTLKA----SLG-TTKYCSYS--GPSS 110

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 62.9 bits (154), Expect = 1e-12
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA--- 394
           +IFV  LS   T +D+   FE++G + + +L  DK T++ +GF  VTF   +   +    
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 395 -YQHLDG 400
            +  ++ 
Sbjct: 61  HFHEINN 67

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 50.5 bits (122), Expect = 3e-08
 Identities = 13/79 (16%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++  L+ N+T + ++ +F++ G +    +    D  +  +    G+GFV F + + + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAML--MFDKTT-NR--HRGFGFVTFESEDIVEK 56

Query: 643 ALKVLQNSSLDEHQIELKR 661
             ++     ++   +E K+
Sbjct: 57  VCEI-HFHEINNKMVECKK 74

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.1 bits (95), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRA 744
           KI V  +       +V+  F+ FG++    L   M    +  HRGFGFV F +++  ++ 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAML---MFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 745 MKA 747
            + 
Sbjct: 58  CEI 60

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 63.8 bits (156), Expect = 2e-12
 Identities = 15/98 (15%), Positives = 34/98 (34%), Gaps = 2/98 (2%)

Query: 321 KSQEDSVQFAEDIAESG-RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG 379
           K+     Q A+   +    +++ NL  ++ E +L  + + +G +    +  D  +  ++G
Sbjct: 9   KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRG 67

Query: 380 FALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
                    E       H +G           P +P  
Sbjct: 68  VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLL 105

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.0 bits (141), Expect = 1e-10
 Identities = 20/105 (19%), Positives = 44/105 (41%), Gaps = 5/105 (4%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
           S+ +   +A+ V+ + +   +Q  + + + N+P    + E+E + K FG++   R+   +
Sbjct: 2   SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRI---L 58

Query: 722 V-GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
              SG  RG GF    +  + +  +        +     V    E
Sbjct: 59  RDSSGTSRGVGFARMESTEKCEAVIGHF-NGKFIKTPPGVSAPTE 102

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 55.7 bits (135), Expect = 1e-09
 Identities = 17/85 (20%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
            +++ +  T LYI NL  +  E  +    K  G + S  + R       G   S G GF 
Sbjct: 18  AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS----GT--SRGVGFA 71

Query: 633 QFYTRESLNQALKVLQNSSLDEHQI 657
           +  + E     +       +     
Sbjct: 72  RMESTEKCEAVIGHFNGKFIKTPPG 96

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.3 bits (108), Expect = 5e-06
 Identities = 9/64 (14%), Positives = 26/64 (40%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            + +++L+   +  G V   ++   + G  R   F      ++ +A + +FN  ++ + 
Sbjct: 35 LSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP 94

Query: 87 RIKV 90
              
Sbjct: 95 PGVS 98

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 63.6 bits (155), Expect = 2e-12
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 3/93 (3%)

Query: 325 DSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVT 384
            S +      +   + V  + ++  E+D+   F        V L  D    +  G  LV 
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRV-DAVHLLKDHVG-RNNGNGLVK 62

Query: 385 FLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
           FL P+   +A +  +  + + R + + P   ++
Sbjct: 63  FLSPQDTFEALK-RNRMLMIQRYVEVSPATERQ 94

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 62.8 bits (153), Expect = 3e-12
 Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 5/91 (5%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + V  +PF A +++V + F     +  V L K     G + G G V+F++  +   A+K 
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH--VGRNNGNGLVKFLSPQDTFEALK- 74

Query: 748 LCQSTHLYGRRLVLEWAEEADNVEDIRKRTN 778
                 +  R + +  A E   V      T+
Sbjct: 75  -RNRMLMIQRYVEVSPATERQWVAAGGHITS 104

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 60.5 bits (147), Expect = 2e-11
 Identities = 14/90 (15%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
               D  + +  + F++ E+ +R  F     + +V + +    +      + G G V+F 
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGR------NNGNGLVKFL 64

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNRN 665
           + +   +ALK      + +  +E+  +   
Sbjct: 65  SPQDTFEALK-RNRMLMIQRYVEVSPATER 93

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 55.9 bits (135), Expect = 7e-10
 Identities = 16/102 (15%), Positives = 36/102 (35%), Gaps = 10/102 (9%)

Query: 207 SDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TTFLGM 260
           S  S  P+   P        + V  +P    + D++ +F  L + +V           G 
Sbjct: 3   SGSSGKPLPINPDD----LYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGN 58

Query: 261 AYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSG 302
             + F   ++  +AL +N+     + + +   ++       G
Sbjct: 59  GLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGG 100

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 9/68 (13%), Positives = 20/68 (29%), Gaps = 2/68 (2%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          +   +  ++  F     V  V L     G+      + +        AL   N   +   
Sbjct: 26 FSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQR 83

Query: 87 RIKVEKCS 94
           ++V   +
Sbjct: 84 YVEVSPAT 91

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 64.1 bits (156), Expect = 3e-12
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
                 V   TG  + +R +P++A ++++   F     ++ V +       G   G   V
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGP--DGRVTGEADV 91

Query: 734 EFITKNEAKRAMK 746
           EF T  EA  AM 
Sbjct: 92  EFATHEEAVAAMS 104

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 62.9 bits (153), Expect = 5e-12
 Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 8/95 (8%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
           + +   +      ++++ L + +TE+ I   F    P+  V +    D +        G 
Sbjct: 36  DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGR------VTGE 88

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
             V+F T E    A+     +++    IEL  ++ 
Sbjct: 89  ADVEFATHEEAVAAMS-KDRANMQHRYIELFLNST 122

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 58.7 bits (142), Expect = 2e-10
 Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 3/84 (3%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
                + +R L Y  TE+D+   F    P+  V + I  +  +  G A V F   E A  
Sbjct: 44  TTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPD-GRVTGEADVEFATHEEAVA 101

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKE 417
           A    D      R + L       
Sbjct: 102 AMS-KDRANMQHRYIELFLNSTTG 124

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.9 bits (127), Expect = 2e-08
 Identities = 17/100 (17%), Positives = 36/100 (36%), Gaps = 6/100 (6%)

Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTT---- 256
           S             S+  V     H + ++ LP    + D+  +F PL    V       
Sbjct: 23  SMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPD 82

Query: 257 --FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSK 294
               G A + F   +    A++K+++  + + + ++  S 
Sbjct: 83  GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNST 122

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 63.4 bits (154), Expect = 3e-12
 Identities = 22/99 (22%), Positives = 34/99 (34%), Gaps = 11/99 (11%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI----ASVTVARKKDPKSPGQFL 625
           E  +    E    + ++ L F +T + +   F +  PI      +      D +      
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR------ 66

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
             G  FV F   E    AL+      L +  IEL RS  
Sbjct: 67  PTGDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRSTA 104

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 61.8 bits (150), Expect = 1e-11
 Identities = 21/117 (17%), Positives = 43/117 (36%), Gaps = 8/117 (6%)

Query: 667 ESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMV 722
            S   T    +  ++K+    + +R +PF A   EV   F     +    + +       
Sbjct: 5   SSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64

Query: 723 GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
           G     G  FV F  +  A+ A++       L  R + L  +  A+  + + + ++ 
Sbjct: 65  GR--PTGDAFVLFACEEYAQNALR--KHKDLLGKRYIELFRSTAAEVQQVLNRFSSA 117

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 60.3 bits (146), Expect = 3e-11
 Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 4/88 (4%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLA---EVILPIDKETDKTKGFALVTFLMPEHA 391
               + +R L +T T +++   F ++ P+    E IL +     +  G A V F   E+A
Sbjct: 22  NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYA 81

Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKENE 419
             A +     +   R + L      E +
Sbjct: 82  QNALR-KHKDLLGKRYIELFRSTAAEVQ 108

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 50.3 bits (120), Expect = 1e-07
 Identities = 14/102 (13%), Positives = 33/102 (32%), Gaps = 11/102 (10%)

Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-----PLASVRTT--- 256
             S           + K     + ++ LP     +++ A+F            +      
Sbjct: 4   GSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63

Query: 257 ---FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKD 295
                G A++ F  E+    AL K+K     + + +++ +  
Sbjct: 64  DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA 105

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 62.7 bits (153), Expect = 4e-12
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           SG IF++NL  ++    L   F  +G +    +  D   + +KG+  V F   E A +A 
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAI 62

Query: 396 QHLDGTVFLGRMLHLIPGKPKEN 418
           + ++G +   R + +   K ++ 
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRKE 85

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 58.4 bits (142), Expect = 1e-10
 Identities = 27/106 (25%), Positives = 49/106 (46%), Gaps = 9/106 (8%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
           P     ++IKNL+ +    ++   F   G I S  V    D        S GYGFV F T
Sbjct: 2   PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENG-----SKGYGFVHFET 54

Query: 637 RESLNQALKVLQNSSLDEHQI--ELKRSNRNLESEATTVKRKSSNV 680
           +E+  +A++ +    L++ ++     +S +  E+E     ++ +NV
Sbjct: 55  QEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNV 100

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 53.0 bits (128), Expect = 9e-09
 Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 9/102 (8%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
             I ++N+        + + F AFG    +   K +      +G+GFV F T+  A+RA+
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGN---ILSCKVVCDENGSKGYGFVHFETQEAAERAI 62

Query: 746 KALCQSTHLYGRRLVLEWAE-----EADNVEDIRKRTNRYFG 782
           + +     L  R++ +   +     EA+     ++ TN Y  
Sbjct: 63  EKM-NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIK 103

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 61.4 bits (150), Expect = 4e-12
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA--- 394
           +IFV  LS    E+ + + F  +G +  + LP+D +T+K +GF  +TF   E   +    
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 395 -YQHLDG 400
            Y ++  
Sbjct: 61  KYHNVGL 67

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 15/79 (18%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++  L+ ++ E+ IR +F   G + S+ +    D K+  +    G+ F+ F   E + +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIEL--PMDNKT-NK--RRGFCFITFKEEEPVKK 56

Query: 643 ALKVLQNSSLDEHQIELKR 661
            ++  +  ++   + E+K 
Sbjct: 57  IMEK-KYHNVGLSKCEIKV 74

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 41.7 bits (99), Expect = 3e-05
 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           KI V  +     + ++ E F  FGE++ + LP     +   RGF F+ F  +   K+ M+
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD-NKTNKRRGFCFITFKEEEPVKKIME 59

Query: 747 A 747
            
Sbjct: 60  K 60

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 61.9 bits (151), Expect = 4e-12
 Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 15/98 (15%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           E R P    TLY+   +   T   +R  F   G I  +++   +              FV
Sbjct: 8   ERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR-----------NCAFV 54

Query: 633 QFYTRESLNQALKVLQNSSLDEHQI--ELKRSNRNLES 668
            +   ES +QA+  L  + ++  Q+   + R    L+S
Sbjct: 55  TYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDS 92

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 61.5 bits (150), Expect = 6e-12
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V      +T   L   F  +G + ++ +   +        A VT+   E A QA   L
Sbjct: 18  LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAEL 69

Query: 399 DGTVFLGRMLHLIPGKPKEN 418
           +GT      L +   + +  
Sbjct: 70  NGTQVESVQLKVNIARKQPM 89

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 8/66 (12%)

Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
            +   F  FG +  + +          R   FV +     A +A+  L   T +   +L 
Sbjct: 29  LLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMESADQAVAEL-NGTQVESVQLK 80

Query: 761 LEWAEE 766
           +  A +
Sbjct: 81  VNIARK 86

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 12/86 (13%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             +T   L+  F   G + D+ +        R  AF+ Y + + A  A+   N T V S 
Sbjct: 23  EDMTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAELNGTQVESV 77

Query: 87  RIKVEKCSNLGDTTKPKSWSKYAPDS 112
           ++KV    N+    + +      P S
Sbjct: 78  QLKV----NIA---RKQPMLDSGPSS 96

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 61.7 bits (150), Expect = 6e-12
 Identities = 12/92 (13%), Positives = 37/92 (40%), Gaps = 9/92 (9%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
                 ++++ ++++V  +P      ++++  +  G++ +  + +         G G VE
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 56

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           F+ K +   A++ L  +T          +   
Sbjct: 57  FVRKEDMTYAVRKL-DNTKFRSHEGETAYIRV 87

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 59.8 bits (145), Expect = 3e-11
 Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 7/80 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V  L  + +  DL     + G +    +          G  +V F+  E  T A + 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTYAVRK 69

Query: 398 LDGTVFLGRMLHLIPGKPKE 417
           LD T F          + K 
Sbjct: 70  LDNTKFRSHEGETAYIRVKV 89

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 55.2 bits (133), Expect = 2e-09
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 12/85 (14%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                +  + +  L  + +   ++ H ++ G +    V R             G G V+F
Sbjct: 10  PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------------GTGVVEF 57

Query: 635 YTRESLNQALKVLQNSSLDEHQIEL 659
             +E +  A++ L N+    H+ E 
Sbjct: 58  VRKEDMTYAVRKLDNTKFRSHEGET 82

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 45.9 bits (109), Expect = 3e-06
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
           RS+  ++V  LP      DLK      GD+    V   G TG+VEF++K     A   L 
Sbjct: 13  RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 71

Query: 505 YTKFKEVPLYLEWA 518
            TKF+       + 
Sbjct: 72  NTKFRSHEGETAYI 85

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 61.4 bits (149), Expect = 1e-11
 Identities = 21/97 (21%), Positives = 33/97 (34%), Gaps = 8/97 (8%)

Query: 323 QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFAL 382
              S      ++ S  + VR L  +V E DL +  EK+G +  V++         K  AL
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQAL 55

Query: 383 VTFLMPEHATQAYQHLDGTVFL--GRMLHLIPGKPKE 417
           V F   + A +             G+         K 
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR 92

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 55.6 bits (134), Expect = 1e-09
 Identities = 15/91 (16%), Positives = 35/91 (38%), Gaps = 9/91 (9%)

Query: 677 SSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
           S +  K + S ++ VR +     ++++ E  + FG + +V +          +    VEF
Sbjct: 6   SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-------FKRQALVEF 58

Query: 736 ITKNEAKRAMKALCQSTHLY-GRRLVLEWAE 765
              + AK  +           G++    ++ 
Sbjct: 59  ENIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 53.6 bits (129), Expect = 4e-09
 Identities = 12/92 (13%), Positives = 27/92 (29%), Gaps = 13/92 (14%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           +      ++++ L  +  E  +    +K G I  V +   K               V+F 
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-----------RQALVEFE 59

Query: 636 TRESLNQALKVLQNS--SLDEHQIELKRSNRN 665
             +S  + +    +    +   Q     S   
Sbjct: 60  NIDSAKECVTFAADVPVYIAGQQAFFNYSTSK 91

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 52.1 bits (125), Expect = 2e-08
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
            ++ V+ L    +  DL    E FG +  V++ P+    LVEF   + AK      A   
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 508 F--KEVPLYLEWA 518
                   +  ++
Sbjct: 76  VYIAGQQAFFNYS 88

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 38.6 bits (90), Expect = 7e-04
 Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 7/67 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT--YVF 84
            + +  L    E+ GT+  V +       F+R A + +   D A+  + +  +   Y+ 
Sbjct: 25 ESVVEADLVEALEKFGTICYVMMM-----PFKRQALVEFENIDSAKECVTFAADVPVYIA 79

Query: 85 SSRIKVE 91
            +    
Sbjct: 80 GQQAFFN 86

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 60.8 bits (148), Expect = 1e-11
 Identities = 12/69 (17%), Positives = 29/69 (42%), Gaps = 1/69 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYG-PLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +++ +L   + E+ +++ F   G  +  V +  ++ T    G+  V F     A +    
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 398 LDGTVFLGR 406
           ++G    G 
Sbjct: 72  INGKPLPGA 80

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                 +L++ +L     E+ I R F   G  + SV + R +           GY FV+F
Sbjct: 5   SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGI-----PAGYCFVEF 59

Query: 635 YTRESLNQALKVLQNSSLD 653
               +  + L  +    L 
Sbjct: 60  ADLATAEKCLHKINGKPLP 78

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 12/72 (16%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 678 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFI 736
           S+ +    + + + ++     ++ +   F   GE +  V++ +  + +G+  G+ FVEF 
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL-TGIPAGYCFVEFA 60

Query: 737 TKNEAKRAMKAL 748
               A++ +  +
Sbjct: 61  DLATAEKCLHKI 72

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
           S   S        E G++FV  L ++ T++ L   F +YG + + ++  DK T++++GF 
Sbjct: 2   SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 382 LVTFLMPEHATQA----YQHLDG 400
            V F  P             LDG
Sbjct: 62  FVKFKDPNCVGTVLASRPHTLDG 84

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 57.6 bits (140), Expect = 2e-10
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 6/95 (6%)

Query: 567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
                      +    L++  L++++T++++R +F + G +    +   KD  +  Q  S
Sbjct: 3   SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVI--MKDKTT-NQ--S 57

Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKR 661
            G+GFV+F     +   L   +  +LD   I+ K 
Sbjct: 58  RGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP 91

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 36/130 (27%), Positives = 62/130 (47%), Gaps = 17/130 (13%)

Query: 557 DNQQGVPEVEENV-EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 615
               G+ +  E V  E ++RE E    L+I  L+F +TE+S+R ++++ G +    V   
Sbjct: 3   SGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV--M 60

Query: 616 KDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKR 675
           +DP S  +  S G+GFV F +   ++ A+   +  S+D   +E KR           V R
Sbjct: 61  RDPAS-KR--SRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR----------AVAR 106

Query: 676 KSSNVAKQTG 685
           + S     +G
Sbjct: 107 EESGSGPSSG 116

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.8 bits (143), Expect = 9e-11
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +  ++F+  LS+  TE+ L   +E++G L + ++  D  + +++GF  VTF        A
Sbjct: 26  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85

Query: 395 ----YQHLDG 400
                  +DG
Sbjct: 86  MAARPHSIDG 95

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 47.7 bits (114), Expect = 7e-07
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 1/86 (1%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
            +  +E    TV  +     K+   K+ +  + F+  +  +   ++ +G+L    +  + 
Sbjct: 4   GSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV-MRD 62

Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKA 747
             S   RGFGFV F +  E   AM A
Sbjct: 63  PASKRSRGFGFVTFSSMAEVDAAMAA 88

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
              ++F+  LS+  T++ L + F ++G + E ++  D  T +++GF  VTF+      + 
Sbjct: 24  SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83

Query: 395 ----YQHLDG 400
                  LD 
Sbjct: 84  LAQSRHELDS 93

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 53.8 bits (130), Expect = 4e-09
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 6/89 (6%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
                     ++I  L++ +T++ +R +F + G +    V   +DP +  +  S G+GFV
Sbjct: 18  GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV--MRDPLT-KR--SRGFGFV 72

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKR 661
            F  +  +++ L       LD   I+ K 
Sbjct: 73  TFMDQAGVDKVLAQ-SRHELDSKTIDPKV 100

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
              +G K+ +  + +Q  Q  + E F  FGE+K   +  +   +   RGFGFV F+ +  
Sbjct: 21  MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAG 79

Query: 741 AKRAMKA 747
             + +  
Sbjct: 80  VDKVLAQ 86

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 59.0 bits (144), Expect = 2e-11
 Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA--- 394
           ++F+  LS+  T++ L + F ++G + E ++  D  T +++GF  VTF+      +    
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 395 -YQHLDG 400
               LD 
Sbjct: 62  SRHELDS 68

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 54.4 bits (132), Expect = 9e-10
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++I  L++ +T++ +R +F + G +    V   +DP +  +  S G+GFV F  +  +++
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLV--MRDPLT-KR--SRGFGFVTFMDQAGVDK 57

Query: 643 ALKVLQNSSLDEHQIELKR 661
            L       LD   I+ K 
Sbjct: 58  VLAQ-SRHELDSKTIDPKV 75

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 40.6 bits (96), Expect = 8e-05
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ +  + +Q  Q  + E F  FGE+K   +  +   +   RGFGFV F+ +    + + 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 747 A 747
            
Sbjct: 61  Q 61

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 59.9 bits (146), Expect = 3e-11
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 326 SVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
           S      + ++  + V  L +  TE DL + F  +G +  V +  D +T  +KGF  V F
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 386 LMPEHATQA---YQHLDG 400
              E   +       +DG
Sbjct: 65  TEYETQVKVMSQRHMIDG 82

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 57.2 bits (139), Expect = 3e-10
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 7/87 (8%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           R  +  + L +  L + +TE  ++ +F   G +  V V  KKD K+ G   S G+GFV+F
Sbjct: 10  RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV--KKDLKT-GH--SKGFGFVRF 64

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKR 661
              E+  + +   Q   +D    + K 
Sbjct: 65  TEYETQVKVMS--QRHMIDGRWCDCKL 89

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 41.4 bits (98), Expect = 8e-05
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
                 A Q  S ++V  +P++  + +++E F  FGE+  V++ KK + +G  +GFGFV 
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHSKGFGFVR 63

Query: 735 FITKNEAKRAMKA 747
           F       + M  
Sbjct: 64  FTEYETQVKVMSQ 76

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 59.6 bits (145), Expect = 3e-11
 Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +FV      V    L++ F  +GP+A V+  +DK+      FA+V              
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVV--MDKD---KGVFAIVEMGDVGAREAVLS- 63

Query: 398 LDGTVFLGRMLHLIPGKPKE 417
                  G  L + P + KE
Sbjct: 64  QSQHSLGGHRLRVRPREQKE 83

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 11/80 (13%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           ++++           +  +F   GP+ASV + + K            +  V+     +  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKG----------VFAIVEMGDVGARE 59

Query: 642 QALKVLQNSSLDEHQIELKR 661
             L      SL  H++ ++ 
Sbjct: 60  AVLS-QSQHSLGGHRLRVRP 78

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 10/74 (13%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V   P     +++ E F AFG +  V + K          F  VE       +    
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD------KGVFAIVEMGDVGARE---A 60

Query: 747 ALCQSTH-LYGRRL 759
            L QS H L G RL
Sbjct: 61  VLSQSQHSLGGHRL 74

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 59.1 bits (144), Expect = 3e-11
 Identities = 21/90 (23%), Positives = 46/90 (51%), Gaps = 6/90 (6%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
           +  +  E    +++  L++++++  ++ +F K G +   T+  K DP + G+  S G+GF
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI--KMDPNT-GR--SRGFGF 57

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKR 661
           + F    S+ + L   +   LD   I+ K+
Sbjct: 58  ILFKDAASVEKVLDQ-KEHRLDGRVIDPKK 86

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++G++FV  LS+  ++ DL   F K+G + +  + +D  T +++GF  + F       + 
Sbjct: 10  DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV 69

Query: 395 ----YQHLDG 400
                  LDG
Sbjct: 70  LDQKEHRLDG 79

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 41.4 bits (98), Expect = 6e-05
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            K+ V  + +   + ++++ F  FGE+    + K    +G  RGFGF+ F      ++ +
Sbjct: 12  GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI-KMDPNTGRSRGFGFILFKDAASVEKVL 70

Query: 746 KA 747
             
Sbjct: 71  DQ 72

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 59.1 bits (143), Expect = 7e-11
 Identities = 13/105 (12%), Positives = 41/105 (39%), Gaps = 12/105 (11%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
            +    ++++ ++++V  +P      ++++  +  G++ +  + +         G G VE
Sbjct: 6   GRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 57

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
           F+ K +   A++ L  +T          +        D  +  + 
Sbjct: 58  FVRKEDMTYAVRKL-DNTKFRSHEGETAYIRVK---VDGPRSPSY 98

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 57.5 bits (139), Expect = 2e-10
 Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 7/80 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V  L  + +  DL     + G +    +          G  +V F+  E  T A + 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTYAVRK 70

Query: 398 LDGTVFLGRMLHLIPGKPKE 417
           LD T F          + K 
Sbjct: 71  LDNTKFRSHEGETAYIRVKV 90

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 54.4 bits (131), Expect = 3e-09
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 12/87 (13%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                +  + +  L  + +   ++ H ++ G +    V R             G G V+F
Sbjct: 11  PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------------GTGVVEF 58

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKR 661
             +E +  A++ L N+    H+ E   
Sbjct: 59  VRKEDMTYAVRKLDNTKFRSHEGETAY 85

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
           RS+  ++V  LP      DLK      GD+    V   G TG+VEF++K     A   L 
Sbjct: 14  RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 72

Query: 505 YTKFKEVPLYLEWA 518
            TKF+       + 
Sbjct: 73  NTKFRSHEGETAYI 86

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 58.6 bits (142), Expect = 7e-11
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)

Query: 338 RIFVRNL------SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
            I V N+           ++ + K+F K+G +     P  +E  KTKG+  + +  P HA
Sbjct: 17  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHA 74

Query: 392 TQAYQHLDGTVFLGR 406
             A ++ DG     +
Sbjct: 75  VDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 9/70 (12%)

Query: 685 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 738
            S I+V N+P       +  ++ + ++F  FG++     P++    G  +G+ F+E+ + 
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASP 71

Query: 739 NEAKRAMKAL 748
             A  A+K  
Sbjct: 72  AHAVDAVKNA 81

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 44.7 bits (106), Expect = 5e-06
 Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 13/90 (14%)

Query: 570 EEDEEREPEPDTTLYIKNL------NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
           ++  +     D+ + + N+           ++ I + F K G I +        P+  G+
Sbjct: 5   KDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-----PEEDGK 59

Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
             + GY F+++ +      A+K      LD
Sbjct: 60  --TKGYIFLEYASPAHAVDAVKNADGYKLD 87

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 58.0 bits (141), Expect = 8e-11
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
              ++FV   +  +T ++L + F +YG + +V +P        + FA VTF   + A   
Sbjct: 10  HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSL 64

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
               +  +  G  +H+   +PK N+ N
Sbjct: 65  CG--EDLIIKGISVHISNAEPKHNKLN 89

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 49.5 bits (119), Expect = 8e-08
 Identities = 8/88 (9%), Positives = 28/88 (31%), Gaps = 12/88 (13%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
                  + +++     + T + +++ F + G +  V +   K  +         + FV 
Sbjct: 5   HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI--PKPFR--------AFAFVT 54

Query: 634 FYTRESLNQALKVLQNSSLDEHQIELKR 661
           F   +         ++  +    + +  
Sbjct: 55  FADDKVAQSLCG--EDLIIKGISVHISN 80

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
           + S+     GSK+ V          E+++ F  +GE+  V +PK        R F FV F
Sbjct: 2   RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP------FRAFAFVTF 55

Query: 736 ITKNEAKRAMK 746
                A+    
Sbjct: 56  ADDKVAQSLCG 66

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 58.8 bits (142), Expect = 9e-11
 Identities = 17/108 (15%), Positives = 39/108 (36%), Gaps = 10/108 (9%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPGQFLSMGYG 630
             E      + ++ L ++ + + ++     C     +A V     ++ +        G  
Sbjct: 11  GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR------QSGEA 64

Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSS 678
           FV+  + + +  ALK     S+    IE+ +S+R            +S
Sbjct: 65  FVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTEMDWVLKHSGPNS 111

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 57.6 bits (139), Expect = 2e-10
 Identities = 16/100 (16%), Positives = 35/100 (35%), Gaps = 8/100 (8%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
            G  + +R +P+     +V+           +  V       G     G  FVE  ++++
Sbjct: 16  EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR--QSGEAFVELESEDD 73

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
            K A+K   +     G R +  +      ++ + K +   
Sbjct: 74  VKLALK---KDRESMGHRYIEVFKSHRTEMDWVLKHSGPN 110

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 54.9 bits (132), Expect = 2e-09
 Identities = 14/100 (14%), Positives = 30/100 (30%), Gaps = 3/100 (3%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEV--ILPIDKETDKTKG 379
           S    +    +  E   + +R L ++ + +D+            V  +  I     +  G
Sbjct: 3   SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG 62

Query: 380 FALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            A V     +    A +  D      R + +      E +
Sbjct: 63  EAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTEMD 101

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 45.7 bits (108), Expect = 4e-06
 Identities = 11/87 (12%), Positives = 32/87 (36%), Gaps = 10/87 (11%)

Query: 220 HKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA----SVR------TTFLGMAYIGFKDEK 269
              + + + ++ LP     +D++ +     +      V           G A++  + E 
Sbjct: 13  EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72

Query: 270 NCNKALNKNKSFWKGKQLNIYKYSKDN 296
           +   AL K++     + + ++K  +  
Sbjct: 73  DVKLALKKDRESMGHRYIEVFKSHRTE 99

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 7/88 (7%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           + S  +FV   +  +TED+L + F +YG + +V +P        + FA VTF   + A  
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQS 57

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
                +  +  G  +H+   +PK N  +
Sbjct: 58  LCG--EDLIIKGISVHISNAEPKHNSNS 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
                S + V        + E+ E F  +G++  V +PK        R F FV F     
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQI 54

Query: 741 AKRAMK 746
           A+    
Sbjct: 55  AQSLCG 60

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 12/79 (15%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++     + TED +R  F + G +  V +   K  +         + FV F   +    
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFI--PKPFR--------AFAFVTFADDQIAQS 57

Query: 643 ALKVLQNSSLDEHQIELKR 661
                ++  +    + +  
Sbjct: 58  LCG--EDLIIKGISVHISN 74

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 58.3 bits (141), Expect = 1e-10
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RI ++NL    +  DL  L  +              T    G   + F   E   +A + 
Sbjct: 30  RITMKNLPEGCSWQDLKDLARENSL---ETTFSSVNTRDFDGTGALEFPSEEILVEALER 86

Query: 398 LDGTVFLGRMLHL 410
           L+   F G ++ +
Sbjct: 87  LNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 54.4 bits (131), Expect = 3e-09
 Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 8/92 (8%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
                + P     + +KNL    +   ++   ++       T +        G       
Sbjct: 18  GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDG------T 69

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKR 661
           G ++F + E L +AL+ L N       I ++R
Sbjct: 70  GALEFPSEEILVEALERLNNIEFRGSVITVER 101

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 53.7 bits (129), Expect = 5e-09
 Identities = 19/102 (18%), Positives = 39/102 (38%), Gaps = 10/102 (9%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFV 733
               +       +I ++N+P      ++++L +    E  F       V +    G G +
Sbjct: 18  GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSS-----VNTRDFDGTGAL 72

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRK 775
           EF ++     A++ L  +    G  + +   E  DN   IR+
Sbjct: 73  EFPSEEILVEALERL-NNIEFRGSVITV---ERDDNPPPIRR 110

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 6/89 (6%)

Query: 207 SDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL-----GMA 261
           S   VP  S       + + I +KNLP G   +DLK   +   L +  ++       G  
Sbjct: 11  SSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTG 70

Query: 262 YIGFKDEKNCNKALNK-NKSFWKGKQLNI 289
            + F  E+   +AL + N   ++G  + +
Sbjct: 71  ALEFPSEEILVEALERLNNIEFRGSVITV 99

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 339 IFVRNL------SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           I V N+           ++ + K+F K+G +     P  +E  KTKG+  + +  P HA 
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAV 61

Query: 393 QAYQHLDGTVFLGR 406
            A ++ DG     +
Sbjct: 62  DAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 9/69 (13%)

Query: 686 SKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 739
           S I+V N+P       +  ++ + ++F  FG++     P++    G  +G+ F+E+ +  
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASPA 58

Query: 740 EAKRAMKAL 748
            A  A+K  
Sbjct: 59  HAVDAVKNA 67

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 43.5 bits (103), Expect = 8e-06
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 13/80 (16%)

Query: 580 DTTLYIKNL------NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
           D+ + + N+           ++ I + F K G I +        P+  G+  + GY F++
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-----PEEDGK--TKGYIFLE 53

Query: 634 FYTRESLNQALKVLQNSSLD 653
           + +      A+K      LD
Sbjct: 54  YASPAHAVDAVKNADGYKLD 73

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 1/55 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
           +  +  +   F + G +T+        GK + + F+ Y     A  A+   +  
Sbjct: 17 LEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVDAVKNADGY 70

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 57.9 bits (140), Expect = 2e-10
 Identities = 13/94 (13%), Positives = 33/94 (35%), Gaps = 10/94 (10%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPGQFLSMGYG 630
           E E +    +  + L ++ T + +   F  C        +     +D K        G  
Sbjct: 5   EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK------RRGDA 58

Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
            ++  + + + +AL+      + +  +E+   N 
Sbjct: 59  LIEMESEQDVQKALE-KHRMYMGQRYVEVYEINN 91

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 57.2 bits (138), Expect = 2e-10
 Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 8/99 (8%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
               I  + +P+     +V   F           +       G    RG   +E  ++ +
Sbjct: 10  DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK--RRGDALIEMESEQD 67

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
            ++A++   +     G+R V  +    ++V+ + K    
Sbjct: 68  VQKALE---KHRMYMGQRYVEVYEINNEDVDALMKSLQV 103

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 53.3 bits (128), Expect = 5e-09
 Identities = 13/89 (14%), Positives = 30/89 (33%), Gaps = 3/89 (3%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEV--ILPIDKETDKTKGFALVTFLMP 388
           E++ +   I  + L ++ T +D+   F           I  +     K +G AL+     
Sbjct: 6   EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65

Query: 389 EHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
           +   +A           R + +     ++
Sbjct: 66  QDVQKA-LEKHRMYMGQRYVEVYEINNED 93

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 42.9 bits (101), Expect = 3e-05
 Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 10/91 (10%)

Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASV----------RTTFLGMAYIG 264
           SK          I  + LP     +D+  +F    + +                G A I 
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61

Query: 265 FKDEKNCNKALNKNKSFWKGKQLNIYKYSKD 295
            + E++  KAL K++ +   + + +Y+ + +
Sbjct: 62  MESEQDVQKALEKHRMYMGQRYVEVYEINNE 92

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 57.5 bits (139), Expect = 2e-10
 Identities = 18/99 (18%), Positives = 34/99 (34%), Gaps = 8/99 (8%)

Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
               ++         S  + +R L   V E DL +  +++GP++ V++         K  
Sbjct: 6   HHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQ 59

Query: 381 ALVTFLMPEHATQAYQHLDGT--VFLGRMLHLIPGKPKE 417
           ALV F     A  A  +         G    +     ++
Sbjct: 60  ALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 54.0 bits (130), Expect = 3e-09
 Identities = 13/93 (13%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 674 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
                +  K   S ++ +R +     ++++ E  + FG + +V +          +    
Sbjct: 9   MENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-------KKRQAL 61

Query: 733 VEFITKNEAKRAMKALCQST-HLYGRRLVLEWA 764
           VEF     A  A+     +  ++ G    + ++
Sbjct: 62  VEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS 94

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 11/78 (14%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
           D+  +      ++I+ L     E  +    ++ GPI+ V V  KK               
Sbjct: 13  DDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK-----------RQAL 61

Query: 632 VQFYTRESLNQALKVLQN 649
           V+F        A+    +
Sbjct: 62  VEFEDVLGACNAVNYAAD 79

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 47.4 bits (113), Expect = 5e-07
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
            ++ ++ L    +  DL    + FG +  V+V P     LVEF     A  A N  A  +
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQ 81

Query: 508 FKEV--PLYLEWA 518
                 P ++ ++
Sbjct: 82  IYIAGHPAFVNYS 94

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 57.2 bits (138), Expect = 4e-10
 Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 8/94 (8%)

Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
                   S  I +R L   VTE ++  L   +G +  +++       K K  A +    
Sbjct: 23  DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNT 76

Query: 388 PEHATQA--YQHLDGTVFLGRMLHLIPGKPKENE 419
            E A     Y      V  G+ +++     KE +
Sbjct: 77  EEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK 110

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 54.2 bits (130), Expect = 4e-09
 Identities = 15/93 (16%), Positives = 38/93 (40%), Gaps = 9/93 (9%)

Query: 674 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
                + +    S+++ +R +P    + EV  L   FG++  + + K        +   F
Sbjct: 19  SHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAF 71

Query: 733 VEFITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
           +E  T+  A   +      +  L G+ + ++++
Sbjct: 72  IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS 104

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 47.2 bits (112), Expect = 1e-06
 Identities = 12/87 (13%), Positives = 29/87 (33%), Gaps = 11/87 (12%)

Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
             +   D      P   ++I+ L  + TE  +       G + ++ + + K         
Sbjct: 17  RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK--------- 67

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSL 652
                F++  T E+ N  +    + + 
Sbjct: 68  --NQAFIEMNTEEAANTMVNYYTSVTP 92

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 46.8 bits (111), Expect = 2e-06
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
           R+I ++ LP      ++ +L  PFG +  +L+        +E   +  A    N      
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 91

Query: 508 --FKEVPLYLEWA 518
              +  P+Y++++
Sbjct: 92  PVLRGQPIYIQFS 104

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.9 bits (137), Expect = 4e-10
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +    L   V+ + L  + EK G +  +++P +      K ++   +   E + +AY  L
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 83

Query: 399 DGTVFLGRMLHLIP 412
           +G   +  +   I 
Sbjct: 84  NGKEVVDDLGQKIT 97

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 54.9 bits (132), Expect = 2e-09
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 13/85 (15%)

Query: 570 EEDEEREPEPDTTLYIKN--LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 627
            E  E       +L + N  L    + + +    +KCG + ++ +   K           
Sbjct: 15  HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK----------- 63

Query: 628 GYGFVQFYTRESLNQALKVLQNSSL 652
            Y F ++ T E   +A   L    +
Sbjct: 64  PYSFARYRTTEESKRAYVTLNGKEV 88

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 46.8 bits (111), Expect = 1e-06
 Identities = 9/61 (14%), Positives = 25/61 (40%), Gaps = 7/61 (11%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           +    +     ++++  + +  G +  + +P        ++ + F  + T  E+KRA   
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-------NKPYSFARYRTTEESKRAYVT 82

Query: 748 L 748
           L
Sbjct: 83  L 83

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 444 ARSKRIILVKN--LPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
           + + + ++V N  L        L  + E  G +  +L+PP        +    ++K A+ 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYV 81

Query: 502 SLAYTKF-----KEVPLYLEWA 518
           +L   +      +++ LYL + 
Sbjct: 82  TLNGKEVVDDLGQKITLYLNFV 103

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 55.6 bits (134), Expect = 8e-10
 Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 8/98 (8%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
                         S  I +R L   VTE ++  L   +G +  +++       K K  A
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 55

Query: 382 LVTFLMPEHATQA--YQHLDGTVFLGRMLHLIPGKPKE 417
            +     E A     Y      V  G+ +++     KE
Sbjct: 56  FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE 93

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.1 bits (130), Expect = 3e-09
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 9/81 (11%)

Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           S+++ +R +P    + EV  L   FG++  + + K        +   F+E  T+  A   
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAFIEMNTEEAANTM 68

Query: 745 MKALCQST-HLYGRRLVLEWA 764
           +      T  L G+ + ++++
Sbjct: 69  VNYYTSVTPVLRGQPIYIQFS 89

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.9 bits (114), Expect = 4e-07
 Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 13/90 (14%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
             P   ++I+ L  + TE  +       G + ++ + + K              F++  T
Sbjct: 13  GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-----------NQAFIEMNT 61

Query: 637 RESLNQALKVLQNSS--LDEHQIELKRSNR 664
            E+ N  +    + +  L    I ++ SN 
Sbjct: 62  EEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.9 bits (114), Expect = 5e-07
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
           R+I ++ LP      ++ +L  PFG +  +L+        +E   +  A    N      
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76

Query: 508 --FKEVPLYLEWA 518
              +  P+Y++++
Sbjct: 77  PVLRGQPIYIQFS 89

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.8 bits (132), Expect = 1e-09
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 8/95 (8%)

Query: 325 DSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVT 384
            S     D A S  + +R L   VTE ++  L   +G +  +++       K K  A + 
Sbjct: 4   GSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLE 57

Query: 385 FLMPEHATQAYQH--LDGTVFLGRMLHLIPGKPKE 417
               E A     +          + +++     KE
Sbjct: 58  LATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 17/91 (18%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 676 KSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
            S +      S++L +R +P +  ++EV  L   FG++  + + K        +   F+E
Sbjct: 5   SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-------GKNQAFLE 57

Query: 735 FITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
             T+  A   +      + HL  + + ++++
Sbjct: 58  LATEEAAITMVNYYSAVTPHLRNQPIYIQYS 88

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 49.0 bits (117), Expect = 2e-07
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
           R++ ++ LP     T++ AL  PFG +  +L+        +E   +  A    N  +   
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 75

Query: 508 --FKEVPLYLEWA 518
              +  P+Y++++
Sbjct: 76  PHLRNQPIYIQYS 88

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 46.7 bits (111), Expect = 9e-07
 Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 13/95 (13%)

Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
            ++ +  P   L+I+ L    TE  +       G + ++ + + K              F
Sbjct: 7   GDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-----------NQAF 55

Query: 632 VQFYTRESLNQALKVLQNS--SLDEHQIELKRSNR 664
           ++  T E+    +         L    I ++ SN 
Sbjct: 56  LELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH 90

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 55.4 bits (133), Expect = 2e-09
 Identities = 15/95 (15%), Positives = 29/95 (30%), Gaps = 8/95 (8%)

Query: 669 EATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSG 725
           +               G  + +R +P+     +V+              V       G  
Sbjct: 28  QQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR- 86

Query: 726 LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
              G  FVE  ++++ K A+K   +     G R +
Sbjct: 87  -QSGEAFVELGSEDDVKMALK---KDRESMGHRYI 117

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 55.0 bits (132), Expect = 3e-09
 Identities = 16/101 (15%), Positives = 36/101 (35%), Gaps = 10/101 (9%)

Query: 567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPGQ 623
                    E      + ++ L ++ + + ++     C      A V     ++ +    
Sbjct: 31  GRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR---- 86

Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
               G  FV+  + + +  ALK     S+    IE+ +S+R
Sbjct: 87  --QSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHR 124

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 51.5 bits (123), Expect = 5e-08
 Identities = 14/101 (13%), Positives = 31/101 (30%), Gaps = 3/101 (2%)

Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTK 378
           +    S+    +  E   + +R L ++ + +D+            A  +  I     +  
Sbjct: 29  QMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQS 88

Query: 379 GFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
           G A V     +    A +  D      R + +      E +
Sbjct: 89  GEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRTEMD 128

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 45.0 bits (106), Expect = 9e-06
 Identities = 15/113 (13%), Positives = 35/113 (30%), Gaps = 13/113 (11%)

Query: 203 DTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA----SVR---- 254
                               +   + ++ LP     +D++ +     +      V     
Sbjct: 23  SMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYT 82

Query: 255 --TTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSK---DNSAKYSG 302
                 G A++    E +   AL K++     + + ++K  +   D   K+SG
Sbjct: 83  REGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHSG 135

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.0 bits (130), Expect = 3e-09
 Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 6/71 (8%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +    + ++YIK    ++T D I+   +  G + ++ + R             G  FV F
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK------GSIFVVF 59

Query: 635 YTRESLNQALK 645
            + ES  + ++
Sbjct: 60  DSIESAKKFVE 70

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.8 bits (127), Expect = 8e-09
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++++      T DD+ +  E  G +  + +         KG   V F   E A +  +  
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-T 71

Query: 399 DGTVFLGRMLHLIP 412
            G  +    L ++ 
Sbjct: 72  PGQKYKETDLLILF 85

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.4 bits (126), Expect = 1e-08
 Identities = 11/80 (13%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + ++  P  A   +++E  +  G++  +++ +        +G  FV F +   AK+ ++
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKFVE 70

Query: 747 ALCQSTHLYGRRLVLEWAEE 766
                       L++ + ++
Sbjct: 71  T--PGQKYKETDLLILFKDD 88

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 27/58 (46%)

Query: 25 FIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
          F    T + +K   E+KG V ++Q++ T    F+   F+ +   + A+  ++     Y
Sbjct: 19 FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY 76

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 41.6 bits (98), Expect = 7e-05
 Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 6/98 (6%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAK 497
                R + +K  P      D+K   E  G +  + +          +  V F     AK
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 498 AAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 535
                    K+KE  L + +  +    + +E+ + K +
Sbjct: 67  KFVE-TPGQKYKETDLLILFKDDYFAKKNEERKQNKVE 103

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 7/76 (9%)

Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNK 273
             +  ++ +K  P      D+K + +    + +++        F G  ++ F   ++  K
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 274 ALNKNKSFWKGKQLNI 289
            +      +K   L I
Sbjct: 68  FVETPGQKYKETDLLI 83

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPL---AEVILPIDKETDKTKGFALVTFLMPEHATQA 394
            +FV +L+  V +  L + F K  P     +V+L    +T  +KG+  V F       +A
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD---QTGVSKGYGFVKFTDELEQKRA 67

Query: 395 YQHLDGTVFLG-RMLHLIPGKPKENEG 420
                G V LG + + L    PK +  
Sbjct: 68  LTECQGAVGLGSKPVRLSVAIPKASRV 94

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 8/91 (8%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR-KKDPKSPGQFLSMGYGFVQF 634
              P+ +L++ +L  +  +  +   F K  P  S    +   D       +S GYGFV+F
Sbjct: 5   SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYP--SCRGGKVVLDQTG----VSKGYGFVKF 58

Query: 635 YTRESLNQALKVLQNS-SLDEHQIELKRSNR 664
                  +AL   Q +  L    + L  +  
Sbjct: 59  TDELEQKRALTECQGAVGLGSKPVRLSVAIP 89

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 703 EELFKAFGELKF--VRLPKKMV-GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL 759
             L++ F +  +   R  K ++  +G+ +G+GFV+F  + E KRA+     +  L  + +
Sbjct: 24  GMLYEFFVK-VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPV 82

Query: 760 VLEWA 764
            L  A
Sbjct: 83  RLSVA 87

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 55.6 bits (133), Expect = 7e-09
 Identities = 11/79 (13%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + ++  P  A   +++E  +  G++  +++ +        +G  FV F +   AK+ ++ 
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKFVET 169

Query: 748 LCQSTHLYGRRLVLEWAEE 766
                      L++ + ++
Sbjct: 170 P--GQKYKETDLLILFKDD 186

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 51.8 bits (123), Expect = 1e-07
 Identities = 17/117 (14%), Positives = 39/117 (33%), Gaps = 2/117 (1%)

Query: 296 NSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTK 355
            +   S A     +     I+    K   +     ++  ++  ++++      T DD+ +
Sbjct: 69  EALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKE 128

Query: 356 LFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP 412
             E  G +  + +         KG   V F   E A +  +   G  +    L ++ 
Sbjct: 129 WLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF 183

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 45.6 bits (107), Expect = 2e-05
 Identities = 13/59 (22%), Positives = 27/59 (45%)

Query: 24  EFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
            F    T + +K   E+KG V ++Q++ T    F+   F+ +   + A+  ++     Y
Sbjct: 116 GFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY 174

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 44.8 bits (105), Expect = 3e-05
 Identities = 18/105 (17%), Positives = 37/105 (35%), Gaps = 7/105 (6%)

Query: 563 PEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 622
           P        DE +    + ++YIK    ++T D I+   +  G + ++ + R        
Sbjct: 92  PSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH----- 146

Query: 623 QFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE 667
                G  FV F + ES  + ++        E  + +   +    
Sbjct: 147 -KAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDYFA 189

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 42.1 bits (98), Expect = 2e-04
 Identities = 23/171 (13%), Positives = 50/171 (29%), Gaps = 15/171 (8%)

Query: 368 LPIDK----ETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVD 423
           LP DK    +    +G+  +  ++  +           +                     
Sbjct: 29  LPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKS---KAELMEISEDK 85

Query: 424 GKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG 483
            K+    S+   +  ++       R + +K  P      D+K   E  G +  + +    
Sbjct: 86  TKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL 145

Query: 484 I-----TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEK 529
                 +  V F     AK    +    K+KE  L + +  +  +   K +
Sbjct: 146 HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD--YFAKKNE 193

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 52.3 bits (125), Expect = 2e-08
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 4/86 (4%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHAT 392
            S ++FV  L   + ED++T  F ++GPL        +       KG+A + F       
Sbjct: 7   GSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQ 66

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKEN 418
                       G++   +     ++
Sbjct: 67  ALID--ACLEEDGKLYLCVSSPTIKD 90

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.9 bits (98), Expect = 6e-05
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++  L  +  ED I   F++ GP+      + +       F   GY F+ F    S+  
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSY---FPPKGYAFLLFQEESSVQ- 66

Query: 643 ALKVLQNSSLDEHQIELKRSNRNLES 668
              ++     ++ ++ L  S+  ++ 
Sbjct: 67  --ALIDACLEEDGKLYLCVSSPTIKD 90

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 39.2 bits (91), Expect = 7e-04
 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRAM 745
           K+ V  +P    + E+   F+ FG L      K         +G+ F+ F  ++  +  +
Sbjct: 10  KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 746 KA 747
            A
Sbjct: 70  DA 71

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 57.2 bits (137), Expect = 2e-08
 Identities = 89/642 (13%), Positives = 180/642 (28%), Gaps = 176/642 (27%)

Query: 220 HKRQYHTIVVKNLPAGVKK---KDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALN 276
           H+ QY  I+     A V     KD++   K + L+      +    I  KD  +    L 
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSI-LSKEEIDHI----IMSKDAVSGTLRL- 67

Query: 277 KNKSFW--KGKQLNIYKYSKDNSAKYSGAADDNN-NASMENIKAKHWKSQEDSVQFAED- 332
               FW    KQ  + +       K+       N    M  IK +  +    +  + E  
Sbjct: 68  ----FWTLLSKQEEMVQ-------KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR 116

Query: 333 --IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT----KGF---ALV 383
             +    ++F +   Y V+        + Y  L + +L +    +       G     + 
Sbjct: 117 DRLYNDNQVFAK---YNVSR------LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVA 167

Query: 384 TFLMPEHATQAYQHLDGTVF---LGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFN- 439
             +   +  Q    +D  +F   L       P    E    +  ++    + R   + N 
Sbjct: 168 LDVCLSYKVQ--CKMDFKIFWLNLKNC--NSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223

Query: 440 ----QVVEARSKRIILVKNLPYRTL--------PTDLKALFEPFGDLG-RVLVPPYGITG 486
                 ++A  +R++  K      L             A F    +L  ++L+     T 
Sbjct: 224 KLRIHSIQAELRRLLKSKPYE-NCLLVLLNVQNAKAWNA-F----NLSCKILL----TT- 272

Query: 487 LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEE-----E 541
                   + K   + L+      + L                S     ++ +       
Sbjct: 273 --------RFKQVTDFLSAATTTHISL-------------DHHSMTLTPDEVKSLLLKYL 311

Query: 542 GEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSI---- 597
               ++  +E      N + +  + E++ +         T    K++N +     I    
Sbjct: 312 DCRPQDLPRE--VLTTNPRRLSIIAESIRDG------LATWDNWKHVNCDKLTTIIESSL 363

Query: 598 --------RRHFKKCG--PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
                   R+ F +    P              P   LS+ +  V       +   +  L
Sbjct: 364 NVLEPAEYRKMFDRLSVFP---------PSAHIPTILLSLIWFDVIKSDVMVV---VNKL 411

Query: 648 QNSSLDE----------H--QIELKRSNRN--------LESEATTVKRKSSNVAKQTGSK 687
              SL E              +ELK    N        ++         S ++      +
Sbjct: 412 HKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471

Query: 688 ILVRNIPF---QAKQSEVEELF-KAFGELKFVRLPKKMVGSGLHRGFG------------ 731
               +I       +  E   LF   F + +F+   +K+                      
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLE--QKIRHDSTAWNASGSILNTLQQLKF 529

Query: 732 FVEFITKNEAK--RAMKALCQSTHLYGRRLVLEWAEEADNVE 771
           +  +I  N+ K  R + A+          L+   ++  D + 
Sbjct: 530 YKPYICDNDPKYERLVNAILDFLPKIEENLIC--SKYTDLLR 569

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.2 bits (124), Expect = 6e-07
 Identities = 35/231 (15%), Positives = 67/231 (29%), Gaps = 54/231 (23%)

Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVT-VARKKDPKSPGQFL-----SMGYGFVQFYTR 637
           ++ N +    +D  +    K      +  +   KD  S    L     S     VQ +  
Sbjct: 29  FVDNFDCKDVQDMPKSILSK----EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE 84

Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA 697
           E L    K L    +   + E ++ +           R  ++   Q  +K    N+    
Sbjct: 85  EVLRINYKFL----MSPIKTEQRQPSMMTRMYIEQRDRLYNDN--QVFAK---YNVS--- 132

Query: 698 KQSEVEELFKAFGELKFVRLPKK------MVGSG-------------LHRGFGF-VEFIT 737
           +     +L +A  EL+    P K      ++GSG             +     F + ++ 
Sbjct: 133 RLQPYLKLRQALLELR----PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188

Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWAEEAD-------NVEDIRKRTNRYF 781
                     L     L   ++   W   +D        +  I+    R  
Sbjct: 189 LKNCNSPETVLEMLQKLL-YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.4 bits (122), Expect = 1e-06
 Identities = 50/402 (12%), Positives = 109/402 (27%), Gaps = 151/402 (37%)

Query: 508 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGE----EGEEEKKENTAEEDNQQGVP 563
            K+V       P+ + +  KE+       K+   G          K+E   ++       
Sbjct: 35  CKDVQDM----PKSILS--KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK------- 81

Query: 564 EVEENVEED----------EEREPEPDTTLYIKNLN--FNSTE-------------DSIR 598
            VEE +  +          E+R+P   T +YI+  +  +N  +               +R
Sbjct: 82  FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141

Query: 599 RHFKKCGPIASVTV---------------ARKKDPKS--PGQ-F-LSMGYGFVQFYTRES 639
           +   +  P  +V +                     +     + F L++           S
Sbjct: 142 QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN-------CNS 194

Query: 640 LNQALKVLQN--SSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQT------------- 684
               L++LQ     +D +       + N++    +++ +   + K               
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254

Query: 685 ----------GSKILV--RNI---------------------PFQAKQSEVEELFKAFGE 711
                       KIL+  R                              EV+ L   + +
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT--PDEVKSLLLKYLD 312

Query: 712 LKFVRLPK----------KMVGSGLHRGFG-------------------FVEFITKNEAK 742
            +   LP+           ++   +  G                      +  +   E +
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372

Query: 743 RAMKALC---QSTHLYGRRLVLEWAE-EADNVEDIRKRTNRY 780
           +    L     S H+    L L W +    +V  +  + ++Y
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.0 bits (121), Expect = 1e-06
 Identities = 98/694 (14%), Positives = 190/694 (27%), Gaps = 228/694 (32%)

Query: 131 HTKDSKPGK-KSKNDPTFSDFLQ-----LHGKDVSKLLP--LSNKDGE----EKEEEN-- 176
           H  D + G+ + +     S F          KDV  +    LS ++ +     K+  +  
Sbjct: 5   HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64

Query: 177 -------EDESNNQIAHA--DISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTI 227
                    +    +     ++  + Y  L +  K T    PS+          R Y+  
Sbjct: 65  LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIK-TEQRQPSMMTRMYIEQRDRLYNDN 123

Query: 228 VV---KNLPAGVKKKDLKAYFKPL-PLASVRTTFLGMAYIGFKDEKNC--NKALNK---- 277
            V    N+        L+     L P  +V     G+   G    K              
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNV--LIDGVLGSG----KTWVALDVCLSYKVQ 177

Query: 278 ----NKSFWKGKQLNIYKYSKDNS-------------AKYSGAADDNNNASM--ENIK-- 316
                K FW    LN+   +   +               ++  +D ++N  +   +I+  
Sbjct: 178 CKMDFKIFW----LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233

Query: 317 ----------------------AKHWK-----------SQEDSVQFAEDIAESGRIFVRN 343
                                 AK W            ++   V      A +  I + +
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293

Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF--LMPEHAT--QAYQHLD 399
            S T+T D++  L  KY       LP  +E   T    L      + +       ++H++
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLP--REVLTTNPRRLSIIAESIRDGLATWDNWKHVN 351

Query: 400 GTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRT 459
                                               D    ++E+ S     +  L    
Sbjct: 352 -----------------------------------CDKLTTIIES-S-----LNVLE--- 367

Query: 460 LPTDLKALFEPFG----DLGRVLVPP--------YGITGLVE-FLQKNQAKAAFNSLAYT 506
            P + + +F+             +P           I   V   + K        SL   
Sbjct: 368 -PAEYRKMFDRLSVFPPS---AHIPTILLSLIWFDVIKSDVMVVVNKLHKY----SLVEK 419

Query: 507 KFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVE 566
           + KE  + +      ++ E K K              E E     +  +  N      + 
Sbjct: 420 QPKESTISI----PSIYLELKVKL-------------ENEYALHRSIVDHYN------IP 456

Query: 567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
           +  + D+   P  D   Y    +       I  H K       +T+ R         FL 
Sbjct: 457 KTFDSDDLIPPYLDQ--YF--YSH------IGHHLKNIEHPERMTLFRMV-------FLD 499

Query: 627 MGYGFVQ---------FYTRESLNQALKVLQN--SSLDEHQIELKRSNRNLESEATTVKR 675
             + F++         +    S+   L+ L+     + ++  + +R    +      + +
Sbjct: 500 --FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAIL---DFLPK 554

Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEV-EELFKA 708
              N+     + +L   I   A+   + EE  K 
Sbjct: 555 IEENLICSKYTDLL--RIALMAEDEAIFEEAHKQ 586

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.0 bits (121), Expect = 1e-06
 Identities = 63/409 (15%), Positives = 109/409 (26%), Gaps = 135/409 (33%)

Query: 3   NHLSGPVVPRNHISLLDLDEVE-------F-----IYKITQEQLKAKFEEKGTVTDVQLK 50
             L           LL L  V+       F     I   T+ +    F    T T + L 
Sbjct: 236 RLLKSKPYEN---CLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 51  YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNL-----GDTTK--PK 103
           + +               D+ ++ L  + +        +V   +        ++ +    
Sbjct: 293 HHSMT----LT------PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA 342

Query: 104 SWSKYAPDSSAYQKLHNIAPK--QDLKPEHTKDSKPGKKSKNDPTFSDF--LQLHGKDV- 158
           +W  +        KL  I       L+P   +             F              
Sbjct: 343 TWDNW--KHVNCDKLTTIIESSLNVLEPAEYRKM-----------FDRLSVFP---PSAH 386

Query: 159 --SKLLPL--SNKDGEEKEEE----------NEDESNNQIAHADISDMEYLKLKTKSKDT 204
             + LL L   +    +               +    + I+   I    YL+LK K ++ 
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI----YLELKVKLEN- 441

Query: 205 APSDPSVPPVSKAPVHKR---QYHTIVVKNLPAGVKKKDLKA-----YF--------KPL 248
                      +  +H+     Y      N+P      DL       YF        K +
Sbjct: 442 -----------EYALHRSIVDHY------NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI 484

Query: 249 PLA----SVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGK--------QLNIYK-YSKD 295
                    R  FL   ++  K        +  + + W           QL  YK Y  D
Sbjct: 485 EHPERMTLFRMVFLDFRFLEQK--------IRHDSTAWNASGSILNTLQQLKFYKPYICD 536

Query: 296 NSAKYSGAADD--NN--NASMENIKAKHWKSQEDSVQFAEDIAESGRIF 340
           N  KY    +   +         I +K+     D ++ A  +AE   IF
Sbjct: 537 NDPKYERLVNAILDFLPKIEENLICSKY----TDLLRIAL-MAEDEAIF 580

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.8 bits (110), Expect = 3e-05
 Identities = 36/206 (17%), Positives = 65/206 (31%), Gaps = 68/206 (33%)

Query: 16  SLLDLDEVEFIYKI--TQEQLKAKFEEKGTVTDVQL-KYTTEGKFRR------------F 60
           SL++    E    I     +LK K E +  +    +  Y     F              +
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY 474

Query: 61  AFIGYH--REDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSW--SKYAPDSSAYQ 116
           + IG+H    +  +  +  F   ++           +         +   K   DS+A+ 
Sbjct: 475 SHIGHHLKNIEHPE-RMTLFRMVFL-----------DF-------RFLEQKIRHDSTAWN 515

Query: 117 KLHNIAPK-QDLK--PEHTKDSKPGKKSKNDPTFS-------DFLQLHGKDV--SKL--- 161
              +I    Q LK    +  D        NDP +        DFL    +++  SK    
Sbjct: 516 ASGSILNTLQQLKFYKPYICD--------NDPKYERLVNAILDFLPKIEENLICSKYTDL 567

Query: 162 --LPLSNKDGEEKEEENEDESNNQIA 185
             + L  +D    E     E++ Q+ 
Sbjct: 568 LRIALMAEDEAIFE-----EAHKQVQ 588

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 52.9 bits (126), Expect = 8e-08
 Identities = 18/94 (19%), Positives = 30/94 (31%), Gaps = 20/94 (21%)

Query: 581 TTLYIKNLNFNST---------EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
            TLY+  ++             E  IR  F + G I  +     K             GF
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK-----------NCGF 183

Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
           V+F  + +   A + + N +L     +     R 
Sbjct: 184 VKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 46.3 bits (109), Expect = 1e-05
 Identities = 14/125 (11%), Positives = 34/125 (27%), Gaps = 15/125 (12%)

Query: 307 NNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVT---------EDDLTKLF 357
                    + K    +ED         ++  ++V  +   +          E  +  +F
Sbjct: 105 RTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVF 164

Query: 358 EKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
            + G +  +         ++K    V F    +A  A + +     L         + + 
Sbjct: 165 SRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREG 218

Query: 418 NEGNV 422
               V
Sbjct: 219 TGLLV 223

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 43.6 bits (102), Expect = 1e-04
 Identities = 16/90 (17%), Positives = 36/90 (40%), Gaps = 18/90 (20%)

Query: 691 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL-- 748
           +++     +S +  +F   G++  +R  +        +  GFV+F  +  A+ A +A+  
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVES-------KNCGFVKFKYQANAEFAKEAMSN 201

Query: 749 ---------CQSTHLYGRRLVLEWAEEADN 769
                           G  L+++WA E  +
Sbjct: 202 QTLLLPSDKEWDDRREGTGLLVKWANEDPD 231

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 49.6 bits (118), Expect = 2e-07
 Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RI V NL Y VT D L ++F K+G + ++I      T   +  AL+ +  P  A  A   
Sbjct: 30  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLS 85

Query: 398 LDGTVFLGRMLHL 410
           LDG         L
Sbjct: 86  LDGQNIYNACCTL 98

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 42.3 bits (99), Expect = 7e-05
 Identities = 14/92 (15%), Positives = 28/92 (30%), Gaps = 11/92 (11%)

Query: 571 EDEEREPEPDTTL--YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMG 628
           +           L   ++NL +  T D + + F K G +  +    K          +  
Sbjct: 17  DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---------NQF 67

Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQIELK 660
              +Q+    S   A   L   ++      L+
Sbjct: 68  QALLQYADPVSAQHAKLSLDGQNIYNACCTLR 99

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 40.0 bits (93), Expect = 5e-04
 Identities = 18/107 (16%), Positives = 42/107 (39%), Gaps = 12/107 (11%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGELKFVRLP 718
            N  L + A  V    + +A    S +L   V N+ +      + ++F  FG +  +   
Sbjct: 5   GNLALAASAAAV---DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 61

Query: 719 KKMVGSGLHRGFGFVEFITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
            K      ++    +++     A+ A  +L  Q+ +     L ++++
Sbjct: 62  TK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 103

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 50.1 bits (119), Expect = 2e-07
 Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RI V NL Y VT D L ++F K+G + ++I      T   +  AL+ +  P  A  A   
Sbjct: 48  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLS 103

Query: 398 LDGTVFLGRMLHL 410
           LDG         L
Sbjct: 104 LDGQNIYNACCTL 116

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 43.2 bits (101), Expect = 7e-05
 Identities = 14/92 (15%), Positives = 28/92 (30%), Gaps = 11/92 (11%)

Query: 571 EDEEREPEPDTTL--YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMG 628
           +           L   ++NL +  T D + + F K G +  +    K          +  
Sbjct: 35  DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---------NQF 85

Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQIELK 660
              +Q+    S   A   L   ++      L+
Sbjct: 86  QALLQYADPVSAQHAKLSLDGQNIYNACCTLR 117

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 42.4 bits (99), Expect = 1e-04
 Identities = 16/94 (17%), Positives = 37/94 (39%), Gaps = 11/94 (11%)

Query: 676 KSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFG 731
             + +A    S +L   V N+ +      + ++F  FG  LK +   K        +   
Sbjct: 34  VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN------QFQA 87

Query: 732 FVEFITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
            +++     A+ A  +L  Q+ +     L ++++
Sbjct: 88  LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 47.2 bits (112), Expect = 8e-07
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 350 EDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH 409
           E+  T++ EKYG + E+ +  D   D   G   V F   E A +A   L+   F G+ +H
Sbjct: 41  EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 46.2 bits (109), Expect = 3e-06
 Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 5/73 (6%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            + ++N  Y +T D L  +    G +  ++        +    A+V F     A +A   
Sbjct: 27  LLSIQNPLYPITVDVLYTVCNPVGKVQRIV-----IFKRNGIQAMVEFESVLCAQKAKAA 81

Query: 398 LDGTVFLGRMLHL 410
           L+G         L
Sbjct: 82  LNGADIYAGCCTL 94

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 40.1 bits (93), Expect = 4e-04
 Identities = 16/98 (16%), Positives = 37/98 (37%), Gaps = 10/98 (10%)

Query: 668 SEATTVKRKSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 724
           S    + R  +      G+K+L   ++N  +      +  +    G+++ + + K+    
Sbjct: 5   SSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR---- 60

Query: 725 GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
             +     VEF +   A++A  A      +Y     L+
Sbjct: 61  --NGIQAMVEFESVLCAQKAKAA-LNGADIYAGCCTLK 95

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 9/92 (9%)

Query: 322 SQEDSVQFAEDIAESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
             +   +F +       I + NL +   ++  + KL E YG +   IL       + K  
Sbjct: 11  EGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMKSQ 64

Query: 381 ALVTFLMPEHATQA--YQHLDGTVFLGRMLHL 410
           A +     E A     +       F GR + +
Sbjct: 65  AFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 17/105 (16%), Positives = 42/105 (40%), Gaps = 9/105 (8%)

Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKK 720
           S+ +   +      +  +  ++ G  I + N+P      S V +L + +G++K   L + 
Sbjct: 2   SSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR- 60

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQST-HLYGRRLVLEWA 764
                  +   F+E  T+ +A   +    +      GR + ++ +
Sbjct: 61  ------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS 99

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 448 RIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 506
           R+I + NLP+     + +  L EP+G +   ++        +E   +  A A  +     
Sbjct: 26  RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVD----- 80

Query: 507 KFKEVPLYLEWAP 519
              +  L+ +   
Sbjct: 81  HCLKKALWFQGRC 93

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 2/66 (3%)

Query: 346 YTVTEDDLTKLFEKYGPLAEVILP--IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
           Y    +D+     KYG +  + +P  +D       G   V F       +A Q L G  F
Sbjct: 25  YEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF 84

Query: 404 LGRMLH 409
             R++ 
Sbjct: 85  ANRVVV 90

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 447 KRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
           +R++ + +    + L   L  L EPFG +   L+        +E      A+AA +
Sbjct: 15  RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 70

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + ++NL+  +    L  L  ++GPL      +       +G AL  +   E A +A   L
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMAL 63

Query: 399 DGTVFLGRMLHLIPGKPKENE 419
           +  V       +    P ENE
Sbjct: 64  NNCVLANTT--IFAESPSENE 82

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.2 bits (91), Expect = 5e-04
 Identities = 20/93 (21%), Positives = 30/93 (32%), Gaps = 14/93 (15%)

Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKY-----GPLAEVILPIDKETDKTKGFALVTFL 386
             +    + VR L   V ++ LT  FE       GP+            +     ++TF 
Sbjct: 4   GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFR 55

Query: 387 MPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            P  A +     D     G  L L P  P+   
Sbjct: 56  EPADAERVLAQAD-HELHGAQLSLRPAPPRAPA 87

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 39.0 bits (91), Expect = 7e-04
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 350 EDDLTKLFEKYGPLAEVILP-IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRML 408
           E +  +  EKYG + + ++  I    D       + F   E A +A   L+G  F GR++
Sbjct: 27  EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86

Query: 409 H 409
            
Sbjct: 87  K 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	787
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.98
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.95
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.95
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.94
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.94
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.94
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.94
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.94
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.94
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.94
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.93
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.93
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.93
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.93
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.92
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.92
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.92
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.85
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.8
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.77
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.77
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.74
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.73
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.73
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.71
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.71
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.71
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.7
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.7
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.69
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.69
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.69
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.69
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.69
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.69
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.69
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.68
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.68
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.68
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.68
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.68
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.68
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.68
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.67
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.67
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.67
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.67
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.67
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.67
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.67
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.67
2div_A	99	TRNA selenocysteine associated protein; structural	99.67
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.67
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.67
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.67
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.67
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.66
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.66
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.66
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.66
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.66
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.66
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.66
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.66
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.66
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.66
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.66
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.66
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.66
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.66
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.66
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.65
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.65
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.65
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.65
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.65
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.65
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.65
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.65
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.65
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.65
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.65
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.65
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.65
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.65
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.65
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.65
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.65
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.65
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.65
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.65
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.65
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.64
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.64
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.64
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.64
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.64
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.64
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.64
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.64
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.64
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.64
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.64
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.64
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.64
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.63
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.63
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.63
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.63
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.63
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.63
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.63
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.63
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.63
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.63
2div_A	99	TRNA selenocysteine associated protein; structural	99.63
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.63
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.63
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.63
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.63
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.63
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.63
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.63
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.63
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.63
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.62
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.62
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.62
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.62
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.62
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.62
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.62
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.62
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.62
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.62
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.62
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.62
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.62
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.61
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.61
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.61
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.61
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.61
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.61
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.61
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.61
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.61
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.61
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.61
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.61
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.61
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.61
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.61
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.6
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.6
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.6
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.6
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.6
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.6
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.6
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.6
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.6
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.6
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.6
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.6
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.6
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.6
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.6
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.6
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.59
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.59
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.59
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.59
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.59
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.59
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.59
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.59
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.59
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.59
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.59
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.59
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.58
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.58
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.58
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.58
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.58
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.58
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.58
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.58
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.58
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.58
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.58
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.58
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.58
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.58
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.58
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.58
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.57
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.57
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.57
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.57
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.57
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.57
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.57
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.57
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.56
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.56
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.56
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.56
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.56
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.56
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.56
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.56
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.56
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.56
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.56
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.56
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.56
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.56
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.56
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.56
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.56
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.55
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.55
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.55
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.55
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.55
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.55
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.55
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.55
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.55
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.55
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.55
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.55
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.54
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.54
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.54
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.54
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.54
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.54
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.54
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.54
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.54
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.53
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.53
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.53
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.53
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.53
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.53
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.53
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.53
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.53
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.53
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.53
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.53
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.52
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.52
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.52
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.52
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.52
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.52
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.52
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.52
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.51
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.51
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.26
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.51
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.51
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.5
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.5
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.5
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.5
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.49
1x5p_A	97	Negative elongation factor E; structure genomics,	99.49
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.23
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.49
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.49
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.49
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.48
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.48
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.47
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.46
1x5p_A	97	Negative elongation factor E; structure genomics,	99.46
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.46
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.46
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.46
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.46
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.45
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.45
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.44
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.44
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.44
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.44
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.43
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.43
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.42
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.41
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.41
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.41
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.4
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.4
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.38
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.38
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.37
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.37
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.36
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.36
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.35
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.31
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.3
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.28
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.24
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.23
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.13
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.08
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.06
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.02
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.92
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.83
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.81
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.69
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.69
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.59
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.28
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.25
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.98
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.71
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.43
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.26
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.24
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.15
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.01
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.83
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.63
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.6
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.43
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.36
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.05
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.86
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.77
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.32
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.95
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.06
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	81.45
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	81.08

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=5.9e-41  Score=351.14  Aligned_cols=257  Identities=20%  Similarity=0.286  Sum_probs=231.8

Q ss_pred             hcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCcc
Q psy3345         443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGV  522 (787)
Q Consensus       443 ~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~  522 (787)
                      ...+.++|+|+|||.++++++|+++|+.|| |..+.+..++++|||+|.+.++|.+|+..|+|..+.|++|.|.|.+.  
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~--   94 (284)
T 3smz_A           18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT--   94 (284)
T ss_dssp             HHHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC--
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCC--
Confidence            345679999999999999999999999999 99999998999999999999999999999999999999999998643  


Q ss_pred             ccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHh
Q psy3345         523 FAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK  602 (787)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~  602 (787)
                                                                               .++|||+|||+++++++|+++|+
T Consensus        95 ---------------------------------------------------------~~~l~v~nlp~~~t~~~l~~~f~  117 (284)
T 3smz_A           95 ---------------------------------------------------------DALLCVANLPPSLTQQQFEELVR  117 (284)
T ss_dssp             ---------------------------------------------------------SCEEEEESCCTTCCHHHHHHHHG
T ss_pred             ---------------------------------------------------------CCEEEEcCCCCcCCHHHHHHHHH
Confidence                                                                     36899999999999999999999


Q ss_pred             hcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhhhhhccccccC
Q psy3345         603 KCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAK  682 (787)
Q Consensus       603 ~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~  682 (787)
                      .||.|.++.++.+..     ++.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.+...           ....
T Consensus       118 ~~G~i~~~~i~~~~~-----~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~-----------~~~~  181 (284)
T 3smz_A          118 PFGSLERCFLVYSER-----TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL-----------TPAL  181 (284)
T ss_dssp             GGSCEEEEEEEECTT-----TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGC-----------CTTT
T ss_pred             hcCCeeEEEEEeeCC-----CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC-----------Cccc
Confidence            999999999998765     578999999999999999999999999999999999999876543           1223


Q ss_pred             CCCCEEEEecCCccC-cHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         683 QTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~-t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      .+.++|||+|||..+ |+++|+++|+.||.|.+++|+++  .+|.++|+|||+|.+.++|.+|+..|| |..+.|++|.|
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v  258 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG--QDGQLKGFAVLEYETAEMAEEAQQQAD-GLSLGGSHLRV  258 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEEC--SSCCEEEEEEEECSSHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEEC--CCCCcccEEEEEeCCHHHHHHHHHHhC-CCccCCeEEEE
Confidence            567899999999995 99999999999999999999998  489999999999999999999999997 79999999999


Q ss_pred             EEccccccH-HHHHHHHh
Q psy3345         762 EWAEEADNV-EDIRKRTN  778 (787)
Q Consensus       762 ~~A~~~~~~-~~~~~~~~  778 (787)
                      +||.+++.. ..+.+..+
T Consensus       259 ~~a~~~~~~~~~~~~~~a  276 (284)
T 3smz_A          259 SFCAPGPPGRSMLAALIA  276 (284)
T ss_dssp             EECCSSSCHHHHHHHHHH
T ss_pred             EEecCCCcccchhhhhhH
Confidence            999988763 33444433

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=5.9e-40  Score=345.01  Aligned_cols=249  Identities=20%  Similarity=0.281  Sum_probs=212.2

Q ss_pred             hcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC----CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEe
Q psy3345         443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  518 (787)
Q Consensus       443 ~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~----~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~  518 (787)
                      .....++|+|+|||+++++++|+++|+.||.|..|.+.+    ++++|||+|.+.++|.+|+. ++|..+.|++|.|.++
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC
Confidence            456789999999999999999999999999999999876    46899999999999999995 9999999999999976


Q ss_pred             cCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHH
Q psy3345         519 PEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIR  598 (787)
Q Consensus       519 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~  598 (787)
                      .                                                            .++|||+|||+.+++++|+
T Consensus       116 ~------------------------------------------------------------~~~l~v~nlp~~~t~~~l~  135 (292)
T 2ghp_A          116 T------------------------------------------------------------ECTLWMTNFPPSYTQRNIR  135 (292)
T ss_dssp             C------------------------------------------------------------SCEEEEECCCTTCCHHHHH
T ss_pred             C------------------------------------------------------------CCEEEEECCCCCCCHHHHH
Confidence            2                                                            3689999999999999999


Q ss_pred             HHHhhcC-CeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhhhhhcc
Q psy3345         599 RHFKKCG-PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKS  677 (787)
Q Consensus       599 ~~F~~~G-~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~  677 (787)
                      ++|+.|| .|.++.++.+..      +.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.+.......      
T Consensus       136 ~~f~~~G~~i~~v~i~~~~~------~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~------  203 (292)
T 2ghp_A          136 DLLQDINVVALSIRLPSLRF------NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT------  203 (292)
T ss_dssp             HHHHHTTCCCCEEECC-------------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC------------
T ss_pred             HHHHHhCCCeEEEEEEeCCC------CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc------
Confidence            9999999 999999988764      568999999999999999999999999999999999998765441111      


Q ss_pred             ccccCCCCCEEEEecCCcc-CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC
Q psy3345         678 SNVAKQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG  756 (787)
Q Consensus       678 ~~~~~~~~~~l~V~nLp~~-~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G  756 (787)
                       .....+.++|||+|||.. +|+++|+++|+.||.|.+|+|+++...+|.++|||||+|.+.++|.+|+ .|| +..+.|
T Consensus       204 -~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~-g~~~~g  280 (292)
T 2ghp_A          204 -DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMN-RSLLGN  280 (292)
T ss_dssp             ----CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGT-TEEETT
T ss_pred             -cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hhc-CCEECC
Confidence             123456799999999999 9999999999999999999999985224999999999999999999999 997 799999


Q ss_pred             ceEEEEEcccc
Q psy3345         757 RRLVLEWAEEA  767 (787)
Q Consensus       757 r~l~v~~A~~~  767 (787)
                      ++|.|.||.++
T Consensus       281 ~~i~V~~a~~k  291 (292)
T 2ghp_A          281 REISVSLADKK  291 (292)
T ss_dssp             EEEEEEECCCC
T ss_pred             cEEEEEEecCC
Confidence            99999999976

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=1.2e-37  Score=325.96  Aligned_cols=241  Identities=22%  Similarity=0.299  Sum_probs=216.1

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ..+.++|||+|||+++|+++|+++|+.|| |..+.+      +.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   91 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL   91 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe
Confidence            34678999999999999999999999999 999887      45778999999999999999999999999999999988


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC------CcEE
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITG  486 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a  486 (787)
                      +..                               .++|+|+|||+.+++++|+++|+.||.|..+.+..+      +++|
T Consensus        92 ~~~-------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~a  140 (284)
T 3smz_A           92 QPT-------------------------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYG  140 (284)
T ss_dssp             CCC-------------------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEE
T ss_pred             cCC-------------------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEE
Confidence            542                               478999999999999999999999999998887542      3589


Q ss_pred             EEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccc
Q psy3345         487 LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVE  566 (787)
Q Consensus       487 ~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  566 (787)
                      ||+|.+.++|.+|+..|+|..+.|++|.|.|+.....                                           
T Consensus       141 fV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~-------------------------------------------  177 (284)
T 3smz_A          141 FAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL-------------------------------------------  177 (284)
T ss_dssp             EEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGC-------------------------------------------
T ss_pred             EEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC-------------------------------------------
Confidence            9999999999999999999999999999999854410                                           


Q ss_pred             cccccccccCCCCCCeEEecCCCCCC-CHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHH
Q psy3345         567 ENVEEDEEREPEPDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALK  645 (787)
Q Consensus       567 ~~~~~~~~~~~~~~~~l~V~NLp~~~-t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~  645 (787)
                             .....+.++|||+|||+++ ++++|+++|+.||.|.++.++.+..      +.++|||||+|.+.++|.+|+.
T Consensus       178 -------~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~------g~~~g~afV~f~~~~~A~~A~~  244 (284)
T 3smz_A          178 -------TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD------GQLKGFAVLEYETAEMAEEAQQ  244 (284)
T ss_dssp             -------CTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSS------CCEEEEEEEECSSHHHHHHHHH
T ss_pred             -------CcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCC------CCcccEEEEEeCCHHHHHHHHH
Confidence                   0122456899999999995 9999999999999999999998764      7899999999999999999999


Q ss_pred             HhCCCccCCeEEEEEecCcccc
Q psy3345         646 VLQNSSLDEHQIELKRSNRNLE  667 (787)
Q Consensus       646 ~lng~~l~g~~l~v~~~~~~~~  667 (787)
                      .|||..++|+.|.|.++.+...
T Consensus       245 ~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          245 QADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HHTTCEETTEECEEEECCSSSC
T ss_pred             HhCCCccCCeEEEEEEecCCCc
Confidence            9999999999999999987655

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=7.3e-38  Score=329.04  Aligned_cols=248  Identities=16%  Similarity=0.224  Sum_probs=213.2

Q ss_pred             ccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEe
Q psy3345         332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLI  411 (787)
Q Consensus       332 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~  411 (787)
                      ...+.++|||+|||+++|+++|+++|+.||+|.+|.++.+..+  ++|||||+|.+.++|.+|++ ++|..+.|+.|.|.
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVS  113 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEE
Confidence            3456789999999999999999999999999999999987643  57999999999999999995 99999999999998


Q ss_pred             eCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCC-CeeEEEecC-----CCcE
Q psy3345         412 PGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLVPP-----YGIT  485 (787)
Q Consensus       412 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G-~v~~v~i~~-----~~~~  485 (787)
                      ++.                                .++|+|+|||..+++++|+++|+.|| .|..|.+..     ..++
T Consensus       114 ~~~--------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~  161 (292)
T 2ghp_A          114 HLT--------------------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF  161 (292)
T ss_dssp             ECC--------------------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCE
T ss_pred             ECC--------------------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceE
Confidence            754                                57899999999999999999999999 999999875     4579


Q ss_pred             EEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCCCccc
Q psy3345         486 GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV  565 (787)
Q Consensus       486 a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  565 (787)
                      |||+|.+.++|.+|+..|+|..+.|++|.|.|+.+..-....                                      
T Consensus       162 afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~--------------------------------------  203 (292)
T 2ghp_A          162 AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT--------------------------------------  203 (292)
T ss_dssp             EEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--------------------------------------------
T ss_pred             EEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc--------------------------------------
Confidence            999999999999999999999999999999998544100000                                      


Q ss_pred             ccccccccccCCCCCCeEEecCCCCC-CCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHH
Q psy3345         566 EENVEEDEEREPEPDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQAL  644 (787)
Q Consensus       566 ~~~~~~~~~~~~~~~~~l~V~NLp~~-~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~  644 (787)
                              .....+.++|||+|||+. +++++|+++|++||.|.+++++.+..    .++.++|||||+|.+.++|.+|+
T Consensus       204 --------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~----~tg~~~g~afV~F~~~~~A~~A~  271 (292)
T 2ghp_A          204 --------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK----EHSFNNCCAFMVFENKDSAERAL  271 (292)
T ss_dssp             -----------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC-------CCCEEEEEEESSHHHHHHHG
T ss_pred             --------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCC----cCCCCceEEEEEeCCHHHHHHHH
Confidence                    012345789999999999 99999999999999999999987542    24789999999999999999999


Q ss_pred             HHhCCCccCCeEEEEEecCcc
Q psy3345         645 KVLQNSSLDEHQIELKRSNRN  665 (787)
Q Consensus       645 ~~lng~~l~g~~l~v~~~~~~  665 (787)
                       .|||..++|+.|.|.++.++
T Consensus       272 -~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          272 -QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             -GGTTEEETTEEEEEEECCCC
T ss_pred             -HhcCCEECCcEEEEEEecCC
Confidence             99999999999999998764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.98  E-value=7.3e-32  Score=268.68  Aligned_cols=175  Identities=23%  Similarity=0.405  Sum_probs=155.5

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+++..     ++.++|||||+|.+.++|.+|+..+|+..+.|+.
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~-----tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~   86 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-----TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP   86 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccC-----CCCccccccceeCCHHHHHHHHHHhhhhhcCCcc
Confidence            34568999999999999999999999999999999999876     6789999999999999999999999999999999


Q ss_pred             EEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEec
Q psy3345         657 IELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI  736 (787)
Q Consensus       657 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~  736 (787)
                      |.+.++.......            ....++|||+|||+.+|+++|+++|+.||.|.+|+|+++   .+.++|||||+|.
T Consensus        87 i~~~~~~~~~~~~------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d---~~~~~g~~fV~f~  151 (213)
T 4f02_A           87 VRIMWSQRDPSLR------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD---ENGSKGYGFVHFE  151 (213)
T ss_dssp             CEEEECCCCTHHH------------HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE---TTEEEEEEEEEES
T ss_pred             ccccccccccccc------------ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeecc---CCCCceEEEEEeC
Confidence            9999986544311            123568999999999999999999999999999999988   4568999999999


Q ss_pred             CHHHHHHHHHHhcCCeeecCceEEEEEccccccHHH
Q psy3345         737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVED  772 (787)
Q Consensus       737 ~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~~~  772 (787)
                      +.++|.+|++.|| |..+.|++|.|.||.++.+.+.
T Consensus       152 ~~~~a~~Ai~~ln-g~~~~g~~i~V~~a~~~~~~~~  186 (213)
T 4f02_A          152 TQEAAERAIEKMN-GMLLNDRKVFVGRFKSRKEREA  186 (213)
T ss_dssp             SHHHHHHHHHHHT-TCEETTEECEEEECCCHHHHHH
T ss_pred             CHHHHHHHHHHhC-CCEECCEEEEEEEcCCCcccch
Confidence            9999999999997 7999999999999998765433

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=2e-30  Score=248.00  Aligned_cols=166  Identities=25%  Similarity=0.484  Sum_probs=152.6

Q ss_pred             CeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Q psy3345         581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK  660 (787)
Q Consensus       581 ~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~  660 (787)
                      ++|||+|||+++|+++|+++|++||.|.++.++.++.      +.++|||||+|.+.++|.+|+..|||..+.|+.|.|.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~------~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~   74 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN------NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKIN   74 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-------CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC------CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEE
Confidence            5899999999999999999999999999999998764      5689999999999999999999999999999999999


Q ss_pred             ecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHH
Q psy3345         661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE  740 (787)
Q Consensus       661 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~  740 (787)
                      ++.....            ....+.++|+|+|||..+|+++|+++|++||.|.+++++.+. .+|.++|||||+|.+.++
T Consensus        75 ~~~~~~~------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~  141 (166)
T 3md3_A           75 WAFQSQQ------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDD  141 (166)
T ss_dssp             ECCCCCC------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECT-TTCCEEEEEEEEESCHHH
T ss_pred             EcCCCCC------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecC-CCCCcceEEEEEeCCHHH
Confidence            9865443            234567899999999999999999999999999999999885 689999999999999999


Q ss_pred             HHHHHHHhcCCeeecCceEEEEEccc
Q psy3345         741 AKRAMKALCQSTHLYGRRLVLEWAEE  766 (787)
Q Consensus       741 A~~Al~~l~~~~~~~Gr~l~v~~A~~  766 (787)
                      |.+|+..|| +..+.|++|.|+||++
T Consensus       142 A~~A~~~l~-g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          142 AQNAMDSMQ-GQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHHHHHT-TCEETTEECEEEESCC
T ss_pred             HHHHHHHhC-CCccCCcEEEEEecCC
Confidence            999999997 7999999999999974

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.97  E-value=7.5e-30  Score=244.59  Aligned_cols=165  Identities=23%  Similarity=0.409  Sum_probs=152.5

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEE
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE  658 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~  658 (787)
                      +.++|||+|||+++++++|+++|++||.|.++.++.+..     ++.++|||||+|.+.++|.+|+..|||..+.|+.|.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~   76 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK-----TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK   76 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT-----TTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCC-----CCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEE
Confidence            468999999999999999999999999999999998765     578999999999999999999999999999999999


Q ss_pred             EEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCH
Q psy3345         659 LKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK  738 (787)
Q Consensus       659 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~  738 (787)
                      |.++.+...              ..+.++|+|+|||..+|+++|+++|++||.|.+++++++. .+|.++|||||+|.+.
T Consensus        77 v~~~~~~~~--------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~  141 (168)
T 1b7f_A           77 VSYARPGGE--------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK-LTGRPRGVAFVRYNKR  141 (168)
T ss_dssp             EEECCCCSS--------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT-TTCCEEEEEEEEESSH
T ss_pred             EEecCCCcc--------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcC-CCCCcceEEEEEECCH
Confidence            999875433              2457899999999999999999999999999999999884 5889999999999999


Q ss_pred             HHHHHHHHHhcCCeeecC--ceEEEEEc
Q psy3345         739 NEAKRAMKALCQSTHLYG--RRLVLEWA  764 (787)
Q Consensus       739 ~~A~~Al~~l~~~~~~~G--r~l~v~~A  764 (787)
                      ++|.+|+..|| +..+.|  ++|.|+||
T Consensus       142 ~~A~~A~~~l~-g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          142 EEAQEAISALN-NVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHHHHT-TCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHhc-CCEecCCCeEEEEEeC
Confidence            99999999997 699988  99999997

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.97  E-value=1.7e-29  Score=241.81  Aligned_cols=164  Identities=27%  Similarity=0.453  Sum_probs=150.8

Q ss_pred             CCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Q psy3345         580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIEL  659 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v  659 (787)
                      .++|||+|||+++++++|+++|+.||.|.++.+..++.     ++.++|||||+|.+.++|.+|+..|||..+.|+.|.|
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~-----~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v   76 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-----TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV   76 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTT-----TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----CCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEE
Confidence            58999999999999999999999999999999998764     5789999999999999999999999999999999999


Q ss_pred             EecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHH
Q psy3345         660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN  739 (787)
Q Consensus       660 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~  739 (787)
                      .++.+...              ..+.++|+|+|||..+|+++|+++|++||.|.+++++.+. .+|.++|||||+|.+.+
T Consensus        77 ~~~~~~~~--------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~  141 (167)
T 1fxl_A           77 SYARPSSA--------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ-VTGVSRGVGFIRFDKRI  141 (167)
T ss_dssp             EECCCCCG--------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHH
T ss_pred             EecCCCcc--------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecC-CCCCccceEEEEeCCHH
Confidence            99875433              2356789999999999999999999999999999998884 57899999999999999


Q ss_pred             HHHHHHHHhcCCeeecCc--eEEEEEc
Q psy3345         740 EAKRAMKALCQSTHLYGR--RLVLEWA  764 (787)
Q Consensus       740 ~A~~Al~~l~~~~~~~Gr--~l~v~~A  764 (787)
                      +|.+|++.|| |..+.|+  +|.|+||
T Consensus       142 ~A~~A~~~l~-g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          142 EAEEAIKGLN-GQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHHHT-TCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhc-CCccCCCccceEEEeC
Confidence            9999999997 7999996  4999997

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.97  E-value=2.1e-29  Score=248.09  Aligned_cols=179  Identities=26%  Similarity=0.456  Sum_probs=150.4

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      ..+.++|||+|||+++|+++|+++|+.||.|.++.++.++.     ++.++|||||+|.+.++|.+|+.. ++..+.|+.
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~   83 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-----TKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRV   83 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCC-----CCCccceEEEEeCCHHHHHHHHhc-CCCEECCEE
Confidence            44578999999999999999999999999999999999765     578999999999999999999985 899999999


Q ss_pred             EEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEec
Q psy3345         657 IELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI  736 (787)
Q Consensus       657 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~  736 (787)
                      |.|.++.......        ......+.++|||+|||..+|+++|+++|+.||.|.+++|+.+. .+|.++|||||+|.
T Consensus        84 l~v~~~~~~~~~~--------~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~F~  154 (196)
T 1l3k_A           84 VEPKRAVSREDSQ--------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFD  154 (196)
T ss_dssp             CEEEECCC-------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT-TTCCEEEEEEEEES
T ss_pred             eeeecccCccccc--------ccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC-CCCCccceEEEEEC
Confidence            9999987543311        11223456899999999999999999999999999999999885 58999999999999


Q ss_pred             CHHHHHHHHHHhcCCeeecCceEEEEEccccccHHH
Q psy3345         737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVED  772 (787)
Q Consensus       737 ~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~~~  772 (787)
                      +.++|.+|+.. + +..+.|+.|.|.||.+++....
T Consensus       155 ~~~~A~~A~~~-~-~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          155 DHDSVDKIVIQ-K-YHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             SHHHHHHHHHC-S-CCEETTEECEEEECC-------
T ss_pred             CHHHHHHHHHh-C-CcEECCEEEEEEecCChhHhcc
Confidence            99999999986 4 6999999999999998886533

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.96  E-value=3.4e-29  Score=250.65  Aligned_cols=179  Identities=21%  Similarity=0.398  Sum_probs=154.9

Q ss_pred             CCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Q psy3345         580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIEL  659 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v  659 (787)
                      .++|||+|||+++|+++|+++|+.||.|.+++++++..     ++.++|||||+|.+.++|.+|+..|||..+.|+.|.|
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v  102 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV-----TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV  102 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-C-----C-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCC-----CCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEE
Confidence            57999999999999999999999999999999998764     5789999999999999999999999999999999999


Q ss_pred             EecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHH
Q psy3345         660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN  739 (787)
Q Consensus       660 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~  739 (787)
                      .++............   ........++|||+|||..+|+++|+++|+.||.|..++|+++. .+|.++|||||+|.+.+
T Consensus       103 ~~~~~~~~~~~~~~~---~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~g~~~g~afV~F~~~~  178 (216)
T 2qfj_A          103 GRPSNIGQAQPIIDQ---LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP-TTGKHKGYGFIEYEKAQ  178 (216)
T ss_dssp             ECCSCCGGGHHHHHH---HHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECT-TTCCEEEEEEEEESSHH
T ss_pred             ecCCCccccchhhhh---hhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecC-CCCCcCceEEEEecCHH
Confidence            988765432211111   11123467899999999999999999999999999999999885 58999999999999999


Q ss_pred             HHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         740 EAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       740 ~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      +|.+|+..|| +..+.|+.|.|.||.+..
T Consensus       179 ~A~~A~~~l~-g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          179 SSQDAVSSMN-LFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHHHHHHHHT-TCBCSSSBCEEEECSSCS
T ss_pred             HHHHHHHHcc-CCEeCCcEEEEEEecCCC
Confidence            9999999997 799999999999998653

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.96  E-value=8.5e-30  Score=243.96  Aligned_cols=166  Identities=27%  Similarity=0.450  Sum_probs=149.7

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEE
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE  658 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~  658 (787)
                      +.++|||+|||+++|+++|+++|++||.|.++++++++.     ++.++|||||+|.+.++|.+|+..  +..++|+.|.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~   74 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPA-----TGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVID   74 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTT-----TSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCC-----CCCccceEEEEEccHHHHHHHHhc--ccccCCeEcc
Confidence            357999999999999999999999999999999998765     678999999999999999999994  6789999999


Q ss_pred             EEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCH
Q psy3345         659 LKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK  738 (787)
Q Consensus       659 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~  738 (787)
                      +.++.....              ..+.++|||+|||..+|+++|+++|++||.|.+++++.+. .+|.++|||||+|.+.
T Consensus        75 v~~~~~~~~--------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~  139 (167)
T 2cjk_A           75 PKRAIPRDE--------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVTYDSA  139 (167)
T ss_dssp             CEECCCHHH--------------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSS-SSSTTSEEEEEEESSH
T ss_pred             cccccchhh--------------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcC-CCCccceEEEEEECCH
Confidence            988765432              1235689999999999999999999999999999999885 5799999999999999


Q ss_pred             HHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         739 NEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       739 ~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      ++|.+|++ ++ +..+.|++|.|.||.|++
T Consensus       140 ~~a~~A~~-~~-~~~~~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          140 DAVDRVCQ-NK-FIDFKDRKIEIKRAEPRH  167 (167)
T ss_dssp             HHHHHHHH-CS-EECSSSSCEEEEECCCCC
T ss_pred             HHHHHHHh-CC-CEEeCCeEEEEeecCCCC
Confidence            99999998 65 799999999999999864

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.96  E-value=7.3e-29  Score=239.41  Aligned_cols=168  Identities=24%  Similarity=0.454  Sum_probs=147.2

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC---Ce
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD---EH  655 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~---g~  655 (787)
                      +.++|||+|||+++|+++|+++|++||.|.+++++++..   .+.+.++|||||+|.+.++|.+|+..|||..+.   ++
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~   78 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS---QNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH   78 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECS---SSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCC---CCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCcc
Confidence            357999999999999999999999999999999999876   222379999999999999999999999998775   67


Q ss_pred             EEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEe
Q psy3345         656 QIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF  735 (787)
Q Consensus       656 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F  735 (787)
                      .+.+.++.....             ...+.++|||+|||..+|+++|+++|++||.|.+++++++  .+|.++|||||+|
T Consensus        79 ~~~~~~~~~~~~-------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~--~~g~~~g~afV~f  143 (175)
T 3nmr_A           79 PIQMKPADSEKN-------------NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG--PDGLSRGCAFVTF  143 (175)
T ss_dssp             CCEEEECGGGCC-------------SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC--TTSCEEEEEEEEE
T ss_pred             ceEEcccccccc-------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEEC--CCCCEEEEEEEEE
Confidence            788877654332             1235678999999999999999999999999999999998  4799999999999


Q ss_pred             cCHHHHHHHHHHhcCCeeec---CceEEEEEcc
Q psy3345         736 ITKNEAKRAMKALCQSTHLY---GRRLVLEWAE  765 (787)
Q Consensus       736 ~~~~~A~~Al~~l~~~~~~~---Gr~l~v~~A~  765 (787)
                      .+.++|.+|+..|| +..+.   |++|.|.||+
T Consensus       144 ~~~~~A~~A~~~l~-g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          144 TTRAMAQTAIKAMH-QAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SSHHHHHHHHHHHT-TSCCCTTCSSCCEEEECC
T ss_pred             CCHHHHHHHHHHhc-CCcccCCCCCCeEEEecC
Confidence            99999999999997 56555   4999999995

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.96  E-value=2.4e-28  Score=243.28  Aligned_cols=166  Identities=20%  Similarity=0.264  Sum_probs=149.1

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|.|++++.+|+++|||||+|.+.++|.+|++.+++..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecC----CCcEEEE
Q psy3345         413 GKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLV  488 (787)
Q Consensus       413 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~----~~~~a~V  488 (787)
                      +...                       .........+|+|+|||+.+++++|+++|+.||.|..|.+..    ++++|||
T Consensus        92 ~~~~-----------------------~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV  148 (213)
T 4f02_A           92 SQRD-----------------------PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFV  148 (213)
T ss_dssp             CCCC-----------------------THHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEE
T ss_pred             cccc-----------------------ccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEE
Confidence            8754                       112233467899999999999999999999999999988865    3468999


Q ss_pred             EeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCc
Q psy3345         489 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  521 (787)
Q Consensus       489 ~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~  521 (787)
                      +|.+.++|.+|+..|||..+.|++|.|.|+...
T Consensus       149 ~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          149 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             EESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             EeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            999999999999999999999999999999543

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.96  E-value=4.8e-28  Score=238.07  Aligned_cols=172  Identities=15%  Similarity=0.193  Sum_probs=143.5

Q ss_pred             CCCeEEecCCC-CCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEE
Q psy3345         579 PDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI  657 (787)
Q Consensus       579 ~~~~l~V~NLp-~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l  657 (787)
                      +.++|||+||| +.+++++|+++|++||.|.+|+++++          ++|||||+|.+.++|..|+..|||..+.|+.|
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----------~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l   72 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----------KPGAAMVEMADGYAVDRAITHLNNNFMFGQKM   72 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----------STTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----------CCCEEEEEECCHHHHHHHHHHhCCCEECCceE
Confidence            56899999999 79999999999999999999999863          36999999999999999999999999999999


Q ss_pred             EEEecCccccchhhh-----------------hhhcc------ccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCe--
Q psy3345         658 ELKRSNRNLESEATT-----------------VKRKS------SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGEL--  712 (787)
Q Consensus       658 ~v~~~~~~~~~~~~~-----------------~~~~~------~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I--  712 (787)
                      .|.++......+...                 ..+..      ......+.++|||+|||+.+|+++|+++|+.||.|  
T Consensus        73 ~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~  152 (205)
T 3tyt_A           73 NVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRP  152 (205)
T ss_dssp             EEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCC
T ss_pred             EEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcce
Confidence            999986432111000                 00000      00112467899999999999999999999999999  


Q ss_pred             eEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc----eEEEEEc
Q psy3345         713 KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR----RLVLEWA  764 (787)
Q Consensus       713 ~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr----~l~v~~A  764 (787)
                      .+++++.+   .|.++|+|||+|.+.++|.+||..|| +..+.|+    ++.|.||
T Consensus       153 ~~v~~~~~---~~~~~g~gfV~f~~~~~A~~Ai~~ln-g~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          153 TSVKVFSG---KSERSSSGLLEWDSKSDALETLGFLN-HYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SEEEECSC---CSSSSEEEEEECSSHHHHHHHHHHHT-TCEECCSSSSSCEECEEE
T ss_pred             EEEEEEcC---CCCCceEEEEEeCCHHHHHHHHHHhC-CCCccCCCCCcceEEEec
Confidence            89999887   36667999999999999999999997 6999986    6888776

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.96  E-value=7.3e-28  Score=231.69  Aligned_cols=159  Identities=23%  Similarity=0.498  Sum_probs=143.7

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhc----C-------CeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHh
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKC----G-------PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL  647 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~----G-------~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~l  647 (787)
                      +.++|||+|||+++|+++|+++|++|    |       .|.++.+..           ++|||||+|.+.++|.+|+ .|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-----------~~g~afV~f~~~~~A~~A~-~~   70 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----------DKNFAFLEFRSVDETTQAM-AF   70 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET-----------TTTEEEEEESSHHHHHHHG-GG
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC-----------CCCEEEEEeCCHHHHHHHH-Hh
Confidence            35899999999999999999999999    6       777777653           5799999999999999999 89


Q ss_pred             CCCccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCC
Q psy3345         648 QNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH  727 (787)
Q Consensus       648 ng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~  727 (787)
                      ||..+.|+.|.|.++.....              ....++|||+|||..+|+++|+++|++||.|.+++++++. .+|.+
T Consensus        71 ~~~~~~g~~i~v~~~~~~~~--------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~g~~  135 (172)
T 2g4b_A           71 DGIIFQGQSLKIRRPHDYQP--------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLS  135 (172)
T ss_dssp             TTCEETTEECEEECCSSCCC--------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TTCSE
T ss_pred             CCcEecCceeeecCCcccCC--------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecC-CCCCc
Confidence            99999999999998754322              2347889999999999999999999999999999999885 58999


Q ss_pred             ceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         728 RGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       728 ~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      +|||||+|.+.++|.+|+..|| +..+.|++|.|+||.
T Consensus       136 ~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          136 KGYAFCEYVDINVTDQAIAGLN-GMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEEEEESSTTHHHHHHHHHT-TCEETTEECEEEECC
T ss_pred             ceEEEEEeCCHHHHHHHHHHcC-CCEECCeEEEEEeCC
Confidence            9999999999999999999997 799999999999984

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.95  E-value=1.9e-28  Score=236.52  Aligned_cols=166  Identities=21%  Similarity=0.377  Sum_probs=143.7

Q ss_pred             CCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCe
Q psy3345         576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH  655 (787)
Q Consensus       576 ~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~  655 (787)
                      ...+.++|||+|||+++++++|+++|+.||.+..+.+ .+..     ++.++|||||+|.+.++|.+|+. |||..+.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~-~~~~-----~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~   81 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVR-----TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN   81 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCC-CEEE-----EETTTTEEEEEESSHHHHHHHHH-GGGEEETTE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEE-EECC-----CCccccEEEEEECCHHHHHHHHh-cCCCEeCCe
Confidence            3456789999999999999999999999997765222 2222     46789999999999999999995 999999999


Q ss_pred             EEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEe
Q psy3345         656 QIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF  735 (787)
Q Consensus       656 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F  735 (787)
                      .|.|.++.....            ....+.++|||+|||..+|+++|+++|++||.|..+    .  .+|.++|||||+|
T Consensus        82 ~l~v~~~~~~~~------------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~--~~~~~~g~afV~f  143 (175)
T 1fje_B           82 EIKLEKPKGRDS------------KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----S--QDGKSKGIAYIEF  143 (175)
T ss_dssp             EEEEECCCCSSC------------STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----C--SSSSCCSEEEEEC
T ss_pred             EEEEecCCCccc------------cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----c--CCCCCceEEEEEE
Confidence            999999875433            122356899999999999999999999999988766    3  4789999999999


Q ss_pred             cCHHHHHHHHHHhcCCeeecCceEEEEEcccc
Q psy3345         736 ITKNEAKRAMKALCQSTHLYGRRLVLEWAEEA  767 (787)
Q Consensus       736 ~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~  767 (787)
                      .+.++|.+|+..|| +..+.|++|.|+||.++
T Consensus       144 ~~~~~A~~A~~~l~-g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          144 KSEADAEKNLEEKQ-GAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             SSHHHHHHHHHHHT-EEEETTEEEEEEECSSC
T ss_pred             CCHHHHHHHHHHhC-CCEECCeEEEEEecCCC
Confidence            99999999999997 79999999999999876

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=2.3e-27  Score=233.80  Aligned_cols=177  Identities=22%  Similarity=0.445  Sum_probs=148.9

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhc----C-------CeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHh
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKC----G-------PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL  647 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~----G-------~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~l  647 (787)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+.           .++|||||+|.+.++|.+|+ .|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----------~~~g~afV~F~~~~~A~~Al-~l   70 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----------QDKNFAFLEFRSVDETTQAM-AF   70 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----------TTTTEEEEEESCSHHHHHHG-GG
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----------CCCCEEEEEeCCHHHHHHHH-Hh
Confidence            35899999999999999999999999    5       56666653           46799999999999999999 89


Q ss_pred             CCCccCCeEEEEEecCccccchhhhhh------hccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEecccc
Q psy3345         648 QNSSLDEHQIELKRSNRNLESEATTVK------RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM  721 (787)
Q Consensus       648 ng~~l~g~~l~v~~~~~~~~~~~~~~~------~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~  721 (787)
                      ||..+.|+.|.|.++............      .........+.++|||+|||..+|+++|+++|++||.|.+++++++.
T Consensus        71 ~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~  150 (198)
T 2yh0_A           71 DGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS  150 (198)
T ss_dssp             TTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECT
T ss_pred             cCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecC
Confidence            999999999999998754331111000      00111223567999999999999999999999999999999999885


Q ss_pred             CCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccccc
Q psy3345         722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       722 ~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~  769 (787)
                       .+|.++|||||+|.+.++|.+|+..|| +..+.|+.|.|+||.++..
T Consensus       151 -~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          151 -ATGLSKGYAFCEYVDINVTDQAIAGLN-GMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             -TTCSEEEEEEEEESSSSHHHHHHHHHT-TCEETTEECEEEESCCCCC
T ss_pred             -CCCCcceEEEEEECCHHHHHHHHHHcC-CCEECCEEEEEEECCCCCC
Confidence             589999999999999999999999997 7999999999999998753

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.95  E-value=3.1e-27  Score=226.33  Aligned_cols=159  Identities=21%  Similarity=0.333  Sum_probs=146.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      ++++|||+|||+++|+++|+++|+.||+|.+|.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46799999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCC------cEEEE
Q psy3345         415 PKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG------ITGLV  488 (787)
Q Consensus       415 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~------~~a~V  488 (787)
                      +..                         ......+|+|+|||..+++++|+++|+.||.|..+.+.++.      ++|||
T Consensus        82 ~~~-------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV  136 (168)
T 1b7f_A           82 PGG-------------------------ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV  136 (168)
T ss_dssp             CCS-------------------------STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEE
T ss_pred             CCc-------------------------ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEE
Confidence            541                         12346889999999999999999999999999999887643      68999


Q ss_pred             EeCCHHHHHHHHHHhcCCeeCC--eeEEEEEe
Q psy3345         489 EFLQKNQAKAAFNSLAYTKFKE--VPLYLEWA  518 (787)
Q Consensus       489 ~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~~  518 (787)
                      +|.+.++|.+|+..|+|..+.|  ++|.|.||
T Consensus       137 ~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          137 RYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999999999987  99999986

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.95  E-value=5.2e-27  Score=224.23  Aligned_cols=159  Identities=24%  Similarity=0.344  Sum_probs=144.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      ++|||+|||+++|+++|+++|++||+|.+|.++.++ ++.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999886 4789999999999999999999999999999999999998765


Q ss_pred             CCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC------CcEEEEEe
Q psy3345         417 ENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEF  490 (787)
Q Consensus       417 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a~V~F  490 (787)
                      ..                       .......+|+|+|||..+++++|+++|+.||.|..+.+..+      +++|||+|
T Consensus        80 ~~-----------------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f  136 (166)
T 3md3_A           80 QQ-----------------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF  136 (166)
T ss_dssp             CC-----------------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEE
T ss_pred             CC-----------------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEe
Confidence            21                       12345678999999999999999999999999999988643      35899999


Q ss_pred             CCHHHHHHHHHHhcCCeeCCeeEEEEEec
Q psy3345         491 LQKNQAKAAFNSLAYTKFKEVPLYLEWAP  519 (787)
Q Consensus       491 ~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  519 (787)
                      .+.++|.+|+..|+|..+.|++|.|.|+.
T Consensus       137 ~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          137 TSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             SCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            99999999999999999999999999984

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.95  E-value=1e-26  Score=222.37  Aligned_cols=158  Identities=20%  Similarity=0.354  Sum_probs=144.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP  415 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  415 (787)
                      .++|||+|||+++|+++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57899999999999999999999999999999999988999999999999999999999999999999999999999875


Q ss_pred             CCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC------CcEEEEE
Q psy3345         416 KENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVE  489 (787)
Q Consensus       416 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a~V~  489 (787)
                      ..                         ......+|+|+|||..+++++|+++|+.||.|..+.+..+      +++|||+
T Consensus        82 ~~-------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~  136 (167)
T 1fxl_A           82 SS-------------------------ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR  136 (167)
T ss_dssp             CC-------------------------GGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEE
T ss_pred             Cc-------------------------ccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEE
Confidence            41                         2234678999999999999999999999999999888653      3689999


Q ss_pred             eCCHHHHHHHHHHhcCCeeCCee--EEEEEe
Q psy3345         490 FLQKNQAKAAFNSLAYTKFKEVP--LYLEWA  518 (787)
Q Consensus       490 F~~~~~A~~A~~~l~~~~~~g~~--l~v~~~  518 (787)
                      |.+.++|.+|+..|+|..+.|+.  |.|.||
T Consensus       137 f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          137 FDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             ESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             eCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            99999999999999999999964  888885

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.95  E-value=1.4e-26  Score=233.15  Aligned_cols=175  Identities=19%  Similarity=0.245  Sum_probs=147.1

Q ss_pred             CCCCCCeEEecCCCC-CCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy3345         576 EPEPDTTLYIKNLNF-NSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDE  654 (787)
Q Consensus       576 ~~~~~~~l~V~NLp~-~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g  654 (787)
                      ...+.++|||+|||+ ++++++|+++|+.||.|.++++..+.          +|||||+|.+.++|.+|+..|||..+.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----------~g~afV~F~~~~~A~~Ai~~l~g~~~~g   99 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----------KENALVQMADGNQAQLAMSHLNGHKLHG   99 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----------SCCEEEEESCHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----------CCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            345678999999999 99999999999999999999998753          5899999999999999999999999999


Q ss_pred             eEEEEEecCccccchhh------hhh---------h------ccccccCCCCCEEEEecCCccCcHHHHHHHHHhcC-Ce
Q psy3345         655 HQIELKRSNRNLESEAT------TVK---------R------KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFG-EL  712 (787)
Q Consensus       655 ~~l~v~~~~~~~~~~~~------~~~---------~------~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G-~I  712 (787)
                      +.|.|.++.........      ...         +      ........+.++|||+|||..+|+++|+++|++|| .|
T Consensus       100 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i  179 (229)
T 2adc_A          100 KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV  179 (229)
T ss_dssp             SBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCE
T ss_pred             eEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCe
Confidence            99999998754211000      000         0      00001124579999999999999999999999999 99


Q ss_pred             eEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec-CceEEEEEcccc
Q psy3345         713 KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY-GRRLVLEWAEEA  767 (787)
Q Consensus       713 ~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~-Gr~l~v~~A~~~  767 (787)
                      .+++++.+      .+|||||+|.+.++|.+|+..|| +..+. |++|.|+||++.
T Consensus       180 ~~v~i~~~------~~g~afV~f~~~~~A~~Ai~~l~-g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          180 KGFKFFQK------DRKMALIQMGSVEEAVQALIDLH-NHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EEEEECSS------STTCEEEEESSHHHHHHHHHHHT-TCBSSSSCBCEEEECSSC
T ss_pred             eEEEEEEC------CCcEEEEEECCHHHHHHHHHHHC-CCccCCCCeEEEEEecCC
Confidence            99999664      37899999999999999999997 69999 999999999864

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.95  E-value=7.6e-27  Score=240.04  Aligned_cols=160  Identities=24%  Similarity=0.422  Sum_probs=147.4

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      ..+.++|||+|||+++|+++|+++|+.||.|.++.+.+           ++|||||+|.+.++|..|+..|||..+.|+.
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~   87 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----------DRGFGFIRLESRTLAEIAKAELDGTILKSRP   87 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----------TTTEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----------CCcEEEEEECCHHHHHHHHHHcCCcEECCce
Confidence            45568999999999999999999999999999999864           4699999999999999999999999999999


Q ss_pred             EEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEec
Q psy3345         657 IELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI  736 (787)
Q Consensus       657 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~  736 (787)
                      |.|.++.                    ++++|||+|||..+|+++|+++|+.||.|.+|+|+.+  .+|.++|||||+|.
T Consensus        88 l~v~~a~--------------------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~f~  145 (261)
T 3sde_A           88 LRIRFAT--------------------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD--DRGRATGKGFVEFA  145 (261)
T ss_dssp             CEEEECC--------------------CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE--TTSCEEEEEEEEES
T ss_pred             eEeeecc--------------------cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC--CCCCcCcEEEEEeC
Confidence            9999975                    2568999999999999999999999999999999998  58999999999999


Q ss_pred             CHHHHHHHHHHhcCCeeec---CceEEEEEcccccc
Q psy3345         737 TKNEAKRAMKALCQSTHLY---GRRLVLEWAEEADN  769 (787)
Q Consensus       737 ~~~~A~~Al~~l~~~~~~~---Gr~l~v~~A~~~~~  769 (787)
                      +.++|.+|+..||++..+.   |++|.|.||.+.++
T Consensus       146 ~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          146 AKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             SHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             CHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCc
Confidence            9999999999997667776   99999999987653

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.94  E-value=2.7e-26  Score=239.47  Aligned_cols=175  Identities=23%  Similarity=0.367  Sum_probs=146.9

Q ss_pred             CCCCCeEEecCCCCCCCHHHHH----HHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIR----RHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL  652 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~----~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l  652 (787)
                      ..+.++|||+|||+++++++|+    ++|++||.|.+|++.+        ++.++|||||+|.+.++|.+|+..|||..+
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--------~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   77 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--------SLKMRGQAFVIFKEVSSATNALRSMQGFPF   77 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--------CCCcceEEEEEECCHHHHHHHHHHhcCCee
Confidence            4567899999999999999976    8999999999999886        256899999999999999999999999999


Q ss_pred             CCeEEEEEecCccccchhhh-----------------------hhh-c--------------------------------
Q psy3345         653 DEHQIELKRSNRNLESEATT-----------------------VKR-K--------------------------------  676 (787)
Q Consensus       653 ~g~~l~v~~~~~~~~~~~~~-----------------------~~~-~--------------------------------  676 (787)
                      .|+.|.|.++..........                       ... .                                
T Consensus        78 ~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (282)
T 3pgw_A           78 YDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHM  157 (282)
T ss_pred             CCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccC
Confidence            99999999986543210000                       000 0                                


Q ss_pred             -----------------------------------------cccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEE
Q psy3345         677 -----------------------------------------SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFV  715 (787)
Q Consensus       677 -----------------------------------------~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v  715 (787)
                                                               .......+.++|||+|||..+|+++|+++|+.||.|.+|
T Consensus       158 ~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v  237 (282)
T 3pgw_A          158 PGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEV  237 (282)
T ss_pred             CCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEE
Confidence                                                     000122356889999999999999999999999999999


Q ss_pred             EeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec-CceEEEEEccc
Q psy3345         716 RLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY-GRRLVLEWAEE  766 (787)
Q Consensus       716 ~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~-Gr~l~v~~A~~  766 (787)
                      +|+.+      .+|||||+|.+.++|.+|+..|| +..+. |+.|+|+||+.
T Consensus       238 ~~~~~------~~g~afV~f~~~~~A~~A~~~l~-g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          238 RLVPG------RHDIAFVEFDNEVQAGAARDALQ-GFKITQNNAMKISFAKK  282 (282)
T ss_pred             EEecC------CCcEEEEEeCCHHHHHHHHHHcC-CcEeCCCCEEEEEEecC
Confidence            99876      26899999999999999999997 69999 99999999973

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.94  E-value=2.5e-26  Score=226.05  Aligned_cols=168  Identities=17%  Similarity=0.261  Sum_probs=140.9

Q ss_pred             CCCccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEee
Q psy3345         220 HKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYK  291 (787)
Q Consensus       220 ~~~~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~  291 (787)
                      .....++|||+|||+++|+++|+++|+.||.+ .+.++       ++|+|||+|.+.++|.+|+..++..+.|+.|.|..
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            35678999999999999999999999999988 77776       46899999999999999999989999999999953


Q ss_pred             cccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecC
Q psy3345         292 YSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPID  371 (787)
Q Consensus       292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~  371 (787)
                      ..+....                             .........++|||+|||+++|+++|+++|+.||.|..|.++.+
T Consensus        89 ~~~~~~~-----------------------------~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~  139 (196)
T 1l3k_A           89 AVSREDS-----------------------------QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD  139 (196)
T ss_dssp             CCC----------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEEC
T ss_pred             ccCcccc-----------------------------cccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeec
Confidence            1110000                             00112234579999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCCC
Q psy3345         372 KETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE  417 (787)
Q Consensus       372 ~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  417 (787)
                      ..+|.++|||||+|.+.++|.+|+.. +|..+.|+.|.|.++.+++
T Consensus       140 ~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~  184 (196)
T 1l3k_A          140 RGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQ  184 (196)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC---
T ss_pred             CCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChh
Confidence            88899999999999999999999985 8999999999999998773

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.94  E-value=1.2e-26  Score=228.58  Aligned_cols=171  Identities=19%  Similarity=0.238  Sum_probs=144.9

Q ss_pred             CCeEEecCCCC-CCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEE
Q psy3345         580 DTTLYIKNLNF-NSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE  658 (787)
Q Consensus       580 ~~~l~V~NLp~-~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~  658 (787)
                      .++|||+|||+ ++++++|+++|+.||.|.++++..+.          +|||||+|.+.++|.+|+..|||..+.|+.|.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----------~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~   72 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----------KENALVQMADGNQAQLAMSHLNGHKLHGKPIR   72 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----------SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----------CCEEEEEECCHHHHHHHHHHhCCCeecCeEEE
Confidence            58999999999 99999999999999999999998643          58999999999999999999999999999999


Q ss_pred             EEecCccccchhhhh---------------hhc------cccccCCCCCEEEEecCCccCcHHHHHHHHHhcC-CeeEEE
Q psy3345         659 LKRSNRNLESEATTV---------------KRK------SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVR  716 (787)
Q Consensus       659 v~~~~~~~~~~~~~~---------------~~~------~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G-~I~~v~  716 (787)
                      |.++...........               .+.      .......+.++|||+|||..+|+++|+++|+.|| .|.+++
T Consensus        73 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~  152 (198)
T 1qm9_A           73 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK  152 (198)
T ss_dssp             EEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEE
T ss_pred             EEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEE
Confidence            999875421100000               000      0001124589999999999999999999999999 999999


Q ss_pred             eccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec-CceEEEEEcccc
Q psy3345         717 LPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY-GRRLVLEWAEEA  767 (787)
Q Consensus       717 i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~-Gr~l~v~~A~~~  767 (787)
                      ++.+      .+|+|||+|.+.++|.+|+..|| +..+. |++|.|+||++.
T Consensus       153 i~~~------~~g~afV~f~~~~~A~~A~~~l~-g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          153 FFQK------DRKMALIQMGSVEEAVQALIDLH-NHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             ESST------TSSCEEEECSSHHHHHHHHHHHT-SSCCSSCCSCCEEEECCC
T ss_pred             EEeC------CCcEEEEEeCCHHHHHHHHHHhc-CCccCCCCeEEEEeeccc
Confidence            9765      37899999999999999999997 69999 999999999864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.94  E-value=5.3e-26  Score=227.41  Aligned_cols=174  Identities=23%  Similarity=0.326  Sum_probs=148.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ...++|||+|||+++|+++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34679999999999999999999999999999999999888999999999999999999999999999999999999887


Q ss_pred             CCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC------CcEEE
Q psy3345         414 KPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGL  487 (787)
Q Consensus       414 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a~  487 (787)
                      .......              .............++|+|+|||..+++++|+++|+.||.|..|.+..+      .++||
T Consensus       106 ~~~~~~~--------------~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~af  171 (216)
T 2qfj_A          106 SNIGQAQ--------------PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF  171 (216)
T ss_dssp             SCCGGGH--------------HHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEE
T ss_pred             CCccccc--------------hhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEE
Confidence            6541100              000001123456789999999999999999999999999999998754      46999


Q ss_pred             EEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCc
Q psy3345         488 VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  521 (787)
Q Consensus       488 V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~  521 (787)
                      |+|.+.++|.+|+..|+|..+.|++|.|.|+...
T Consensus       172 V~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~  205 (216)
T 2qfj_A          172 IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP  205 (216)
T ss_dssp             EEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSC
T ss_pred             EEecCHHHHHHHHHHccCCEeCCcEEEEEEecCC
Confidence            9999999999999999999999999999999655

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.94  E-value=3.9e-26  Score=220.20  Aligned_cols=160  Identities=22%  Similarity=0.405  Sum_probs=141.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCC--CcceEEEEEEcCHHHHHHHHHHhCCceeC---CeEEE
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHATQAYQHLDGTVFL---GRMLH  409 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~--~~~g~afV~F~~~~~A~~a~~~l~~~~~~---g~~l~  409 (787)
                      +.++|||+|||+++|+++|+++|++||+|.+|.++.++.++  .++|||||+|.+.++|.+|++.|+|..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46799999999999999999999999999999999998776  89999999999999999999999998775   67888


Q ss_pred             EeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC-----Cc
Q psy3345         410 LIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GI  484 (787)
Q Consensus       410 v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~-----~~  484 (787)
                      +.++....                        .......+|+|+|||..+++++|+++|+.||.|.++.+..+     ++
T Consensus        82 ~~~~~~~~------------------------~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g  137 (175)
T 3nmr_A           82 MKPADSEK------------------------NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRG  137 (175)
T ss_dssp             EEECGGGC------------------------CSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEE
T ss_pred             Eccccccc------------------------cccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEE
Confidence            87765431                        12234678999999999999999999999999999988764     46


Q ss_pred             EEEEEeCCHHHHHHHHHHhcCCeeC---CeeEEEEEe
Q psy3345         485 TGLVEFLQKNQAKAAFNSLAYTKFK---EVPLYLEWA  518 (787)
Q Consensus       485 ~a~V~F~~~~~A~~A~~~l~~~~~~---g~~l~v~~~  518 (787)
                      +|||+|.+.++|.+|+..|+|..+.   +++|.|.|+
T Consensus       138 ~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          138 CAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             EEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            8999999999999999999998776   499999997

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.94  E-value=8.6e-26  Score=217.14  Aligned_cols=159  Identities=18%  Similarity=0.308  Sum_probs=145.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHhhccC----C-------CeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEE
Q psy3345         446 SKRIILVKNLPYRTLPTDLKALFEPF----G-------DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  514 (787)
Q Consensus       446 ~~~~i~v~nlp~~~t~~~l~~~F~~~----G-------~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~  514 (787)
                      ..++|+|+|||+++++++|+++|+.|    |       .|.++.+..++++|||+|.++++|.+|+ .++|..+.|++|.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            46899999999999999999999999    7       8889999999999999999999999999 8999999999999


Q ss_pred             EEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCH
Q psy3345         515 LEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTE  594 (787)
Q Consensus       515 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~  594 (787)
                      |.++....                                                     .....++|||+|||+.+++
T Consensus        82 v~~~~~~~-----------------------------------------------------~~~~~~~l~v~nlp~~~t~  108 (172)
T 2g4b_A           82 IRRPHDYQ-----------------------------------------------------PLPGAHKLFIGGLPNYLND  108 (172)
T ss_dssp             EECCSSCC-----------------------------------------------------CCTTTTCEEEECCCTTCCH
T ss_pred             ecCCcccC-----------------------------------------------------CCCCCCEEEEEcCCCcCCH
Confidence            99864320                                                     1223689999999999999


Q ss_pred             HHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecC
Q psy3345         595 DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN  663 (787)
Q Consensus       595 ~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~  663 (787)
                      ++|+++|++||.|.++.+..++.     ++.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.
T Consensus       109 ~~l~~~f~~~G~v~~v~i~~~~~-----~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          109 DQVKELLTSFGPLKAFNLVKDSA-----TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHHHHHHTTSCEEEEEEEECTT-----TCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHHhcCCceEEEEEecCC-----CCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            99999999999999999998764     57899999999999999999999999999999999999873

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.94  E-value=3.1e-26  Score=219.14  Aligned_cols=159  Identities=19%  Similarity=0.384  Sum_probs=143.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      ++++|||+|||+++|+++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|.+|++  ++..+.|+.|.+.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            35689999999999999999999999999999999998899999999999999999999998  4678999999998876


Q ss_pred             CCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC------CcEEEE
Q psy3345         415 PKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLV  488 (787)
Q Consensus       415 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~a~V  488 (787)
                      +.                         .......+|+|+|||+.+++++|+++|+.||.|..+.+..+      +++|||
T Consensus        80 ~~-------------------------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV  134 (167)
T 2cjk_A           80 PR-------------------------DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV  134 (167)
T ss_dssp             CH-------------------------HHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEE
T ss_pred             ch-------------------------hhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEE
Confidence            42                         12234678999999999999999999999999999998763      369999


Q ss_pred             EeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCc
Q psy3345         489 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  521 (787)
Q Consensus       489 ~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~  521 (787)
                      +|.+.++|.+|+. ++|..+.|++|.|.|+.+.
T Consensus       135 ~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          135 TYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             EECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9999999999998 8999999999999998653

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.93  E-value=3.1e-25  Score=218.00  Aligned_cols=194  Identities=14%  Similarity=0.141  Sum_probs=142.8

Q ss_pred             CCCEEEEeCCC-CCCCHHHHHHhhccCCCeeEEEecCC-CcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccc
Q psy3345         446 SKRIILVKNLP-YRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  523 (787)
Q Consensus       446 ~~~~i~v~nlp-~~~t~~~l~~~F~~~G~v~~v~i~~~-~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~  523 (787)
                      +.++|+|+||| +.+++++|+++|+.||.|.+|.+.++ +++|||+|.+.++|.+|+..|||..+.|++|.|.|+.....
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~   82 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI   82 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCcc
Confidence            46899999999 89999999999999999999998874 68999999999999999999999999999999999864421


Q ss_pred             cccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhh
Q psy3345         524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKK  603 (787)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~  603 (787)
                      ..... .          ..+...     ....+......................+.++|||+|||+++|+++|+++|++
T Consensus        83 ~p~~~-~----------~~~~~~-----~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~  146 (205)
T 3tyt_A           83 MPGQS-Y----------GLEDGS-----CSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDE  146 (205)
T ss_dssp             CCCSC-C----------BCTTSC-----BSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHH
T ss_pred             CCCcc-c----------ccccCC-----ccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHh
Confidence            10000 0          000000     0000000000000000000000112346789999999999999999999999


Q ss_pred             cCCe--EEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCe----EEEEEec
Q psy3345         604 CGPI--ASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH----QIELKRS  662 (787)
Q Consensus       604 ~G~v--~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~----~l~v~~~  662 (787)
                      ||.|  .++++..+.       +.++|||||+|.+.++|.+|+..|||..|.|+    ++.|+++
T Consensus       147 ~G~v~~~~v~~~~~~-------~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          147 LGVKRPTSVKVFSGK-------SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             HTCCCCSEEEECSCC-------SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             cCCcceEEEEEEcCC-------CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            9999  899988653       24569999999999999999999999999886    5666664

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.93  E-value=4.2e-25  Score=217.58  Aligned_cols=182  Identities=16%  Similarity=0.245  Sum_probs=149.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHhhccC----C-------CeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEE
Q psy3345         446 SKRIILVKNLPYRTLPTDLKALFEPF----G-------DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  514 (787)
Q Consensus       446 ~~~~i~v~nlp~~~t~~~l~~~F~~~----G-------~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~  514 (787)
                      ..++|+|+|||+++++++|+++|+.|    |       .|..+.+..++++|||+|.+.++|.+|+ .|+|..+.|++|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            36899999999999999999999999    6       7888888889999999999999999999 8999999999999


Q ss_pred             EEEecCccccccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCH
Q psy3345         515 LEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTE  594 (787)
Q Consensus       515 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~  594 (787)
                      |.|+...........            .+             ..        ............+.++|||+|||+.+++
T Consensus        82 v~~~~~~~~~~~~~~------------~~-------------~~--------~~~~~~~~~~~~~~~~l~v~nl~~~~~~  128 (198)
T 2yh0_A           82 IRRPHDYQPLPGMSE------------NP-------------SV--------YVPGVVSTVVPDSAHKLFIGGLPNYLND  128 (198)
T ss_dssp             EECCCCCCCCCCSSS------------CS-------------SC--------CCTTSSCCCSSCCCCEEEEECCCTTCCH
T ss_pred             EeCCCCCCCCCCCcC------------CC-------------cC--------CCCCCccCCCCCCCCEEEEeCCCCCCCH
Confidence            998854311000000            00             00        0000001123356789999999999999


Q ss_pred             HHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccc
Q psy3345         595 DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNL  666 (787)
Q Consensus       595 ~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~  666 (787)
                      ++|+++|++||.|.++.+..+..     ++.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.+..
T Consensus       129 ~~l~~~f~~~G~v~~~~~~~~~~-----~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          129 DQVKELLTSFGPLKAFNLVKDSA-----TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             HHHHHHHHTBSCEEEEEEEECTT-----TCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             HHHHHHHHHcCCccEEEEeecCC-----CCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99999999999999999998764     57899999999999999999999999999999999999987654

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.93  E-value=8.7e-26  Score=217.75  Aligned_cols=164  Identities=20%  Similarity=0.276  Sum_probs=142.2

Q ss_pred             ccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEe
Q psy3345         332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLI  411 (787)
Q Consensus       332 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~  411 (787)
                      ...+.++|||+|||+++|+++|+++|+.||.+.. .++.+..+|.++|||||+|.+.++|.+|++ |+|..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            3456789999999999999999999999998766 344455678899999999999999999995 99999999999999


Q ss_pred             eCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEec--CCCcEEEEE
Q psy3345         412 PGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVE  489 (787)
Q Consensus       412 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~--~~~~~a~V~  489 (787)
                      ++.+...                       ......++|+|+|||+.+++++|+++|+.||.|..+ ..  ..+++|||+
T Consensus        87 ~~~~~~~-----------------------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~  142 (175)
T 1fje_B           87 KPKGRDS-----------------------KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIE  142 (175)
T ss_dssp             CCCCSSC-----------------------STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEE
T ss_pred             cCCCccc-----------------------cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEE
Confidence            9886521                       123356899999999999999999999999999887 22  255799999


Q ss_pred             eCCHHHHHHHHHHhcCCeeCCeeEEEEEecCc
Q psy3345         490 FLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  521 (787)
Q Consensus       490 F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~  521 (787)
                      |.+.++|.+|+..|+|..+.|++|.|.|+.+.
T Consensus       143 f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          143 FKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999999999653

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.93  E-value=1.8e-24  Score=217.84  Aligned_cols=185  Identities=23%  Similarity=0.218  Sum_probs=148.3

Q ss_pred             ccCCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         332 DIAESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       332 ~~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      ...++++|||+|||+ ++|+++|+++|+.||.|.+|.++.++     +|||||+|.+.++|.+|++.|+|..+.|+.|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345678999999999 99999999999999999999998764     689999999999999999999999999999999


Q ss_pred             eeCCCCCCCCCC----C-CCc-ccccc---cc-ccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCC-CeeEEEe
Q psy3345         411 IPGKPKENEGNV----D-GKV-HCCIS---ER-KLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLV  479 (787)
Q Consensus       411 ~~~~~~~~~~~~----~-~~~-~~a~~---~~-~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G-~v~~v~i  479 (787)
                      .++.........    . ... .....   .. ............+.++|+|+|||..+++++|+++|+.|| .|..|.+
T Consensus       105 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i  184 (229)
T 2adc_A          105 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF  184 (229)
T ss_dssp             ECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEE
T ss_pred             EEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEE
Confidence            998765111000    0 000 00000   00 000000111234579999999999999999999999999 9999999


Q ss_pred             -cCCCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeeEEEEEecCc
Q psy3345         480 -PPYGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAPEG  521 (787)
Q Consensus       480 -~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~~~~~  521 (787)
                       +.++++|||+|.+.++|.+|+..|+|..+. |++|.|.|+.+.
T Consensus       185 ~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          185 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence             447889999999999999999999999999 999999999654

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.92  E-value=1.4e-24  Score=226.41  Aligned_cols=184  Identities=22%  Similarity=0.340  Sum_probs=147.5

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLT----KLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRML  408 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l  408 (787)
                      ..+.++|||+|||+++|+++|+    ++|+.||.|.+|.++.   +|+++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4567899999999999999976    8999999999999875   58899999999999999999999999999999999


Q ss_pred             EEeeCCCCCCC-CCCCCC-------------------------------c-----ccc-----------------cc---
Q psy3345         409 HLIPGKPKENE-GNVDGK-------------------------------V-----HCC-----------------IS---  431 (787)
Q Consensus       409 ~v~~~~~~~~~-~~~~~~-------------------------------~-----~~a-----------------~~---  431 (787)
                      .|.++...... ....+.                               .     ...                 .+   
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            99998664210 000000                               0     000                 00   


Q ss_pred             --------------c---------------cccchhhhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCC
Q psy3345         432 --------------E---------------RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY  482 (787)
Q Consensus       432 --------------~---------------~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~  482 (787)
                                    .               ...............++|+|+|||..+++++|+++|+.||.|.+|.+.++
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~  242 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG  242 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC
Confidence                          0               00000000112335688999999999999999999999999999999886


Q ss_pred             C-cEEEEEeCCHHHHHHHHHHhcCCeeC-CeeEEEEEec
Q psy3345         483 G-ITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAP  519 (787)
Q Consensus       483 ~-~~a~V~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~~~  519 (787)
                      + ++|||+|.+.++|.+|+..|+|..+. |++|.|.|+.
T Consensus       243 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            6 89999999999999999999999999 9999999984

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.92  E-value=1.7e-24  Score=213.18  Aligned_cols=182  Identities=21%  Similarity=0.228  Sum_probs=145.9

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         335 ESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       335 ~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      .+++|||+|||+ ++|+++|+++|+.||.|.+|.++.++     +|||||+|.+.++|.+|++.|+|..+.|+.|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            357999999999 99999999999999999999998764     679999999999999999999999999999999998


Q ss_pred             CCCCCCCCC---C-CCccccccccccchh------hhhhhcCCCCEEEEeCCCCCCCHHHHHHhhccCC-CeeEEEecC-
Q psy3345         414 KPKENEGNV---D-GKVHCCISERKLDAF------NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLVPP-  481 (787)
Q Consensus       414 ~~~~~~~~~---~-~~~~~a~~~~~~~~~------~~~~~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G-~v~~v~i~~-  481 (787)
                      .........   . .......+......+      .......+.++|+|+|||..+++++|+++|+.|| .|..+.+.+ 
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence            765211000   0 000000000000000      0011234578999999999999999999999999 999999954 


Q ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeeEEEEEecCc
Q psy3345         482 YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAPEG  521 (787)
Q Consensus       482 ~~~~a~V~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~~~~~  521 (787)
                      ++++|||+|.+.++|.+|+..|+|..+. |++|.|.|+.+.
T Consensus       157 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            7789999999999999999999999999 999999998654

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.92  E-value=5.9e-24  Score=218.47  Aligned_cols=158  Identities=23%  Similarity=0.327  Sum_probs=144.9

Q ss_pred             cCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccc
Q psy3345         444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  523 (787)
Q Consensus       444 ~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~  523 (787)
                      ....++|+|+|||+++|+++|+++|+.||.|..|.+.+++++|||+|.+.++|.+|+..|+|..+.|++|.|.|+..   
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~---   95 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH---   95 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC---
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc---
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999832   


Q ss_pred             cccccccccccccccccccccchhhhhcccccccccCCCcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhh
Q psy3345         524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKK  603 (787)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~  603 (787)
                                                                              .++|||+|||+.+|+++|+++|+.
T Consensus        96 --------------------------------------------------------~~~l~v~nl~~~~t~~~l~~~F~~  119 (261)
T 3sde_A           96 --------------------------------------------------------GAALTVKNLSPVVSNELLEQAFSQ  119 (261)
T ss_dssp             --------------------------------------------------------SSEEEEESCCTTCCHHHHHHHHGG
T ss_pred             --------------------------------------------------------CCcccccCCCCCCCHHHHHHHHHh
Confidence                                                                    368999999999999999999999


Q ss_pred             cCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhC-CCccC---CeEEEEEecCccc
Q psy3345         604 CGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQ-NSSLD---EHQIELKRSNRNL  666 (787)
Q Consensus       604 ~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~ln-g~~l~---g~~l~v~~~~~~~  666 (787)
                      ||.|.++.++.+.      ++.++|||||+|.+.++|.+|+..|| |..+.   |++|.|.++....
T Consensus       120 ~G~i~~v~i~~~~------~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          120 FGPVEKAVVVVDD------RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             GSCEEEEEEEEET------TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             cCCeEEEEeeeCC------CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            9999999999885      37899999999999999999999995 44544   9999999987653

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.85  E-value=8.2e-21  Score=179.23  Aligned_cols=150  Identities=17%  Similarity=0.253  Sum_probs=114.2

Q ss_pred             EEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhhhhhccccccCCCCCEE
Q psy3345         609 SVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKI  688 (787)
Q Consensus       609 ~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  688 (787)
                      ++.|..+.       ..++|||||+|.+.++|.+|+..+++....+..+.+.......... .............+.++|
T Consensus         2 ~~kl~ln~-------~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l   73 (158)
T 2kn4_A            2 QYKLILNG-------KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT-EGSHHHHHHMDVEGMTSL   73 (158)
T ss_dssp             EEEEEEEC-------SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEE-CCCCCSSCCCCCCBCCEE
T ss_pred             cEEEEecC-------ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccc-ccccccccccCCCCCCEE
Confidence            35555544       2689999999999999999999988754433333332221111100 000011112223467899


Q ss_pred             EEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         689 LVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       689 ~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      ||+|||+.+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|+||.+..
T Consensus        74 ~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           74 KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR-YTKESRGFAFVRFHDKRDAEDAMDAMD-GAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             EEESCCTTCCHHHHHHHHHHHSCEEEEECCCCS-SCTTSCCEEEEEESBHHHHHHHHHHST-TEESSSSEEEEEEECCSS
T ss_pred             EEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC-CCCccceEEEEEECCHHHHHHHHHHhC-CCEECCeEEEEEECCCCC
Confidence            999999999999999999999999999999985 589999999999999999999999997 799999999999998654

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.82  E-value=4.5e-20  Score=172.26  Aligned_cols=136  Identities=18%  Similarity=0.289  Sum_probs=115.0

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHh-CCCccCCeEEEEEecCccccchhh--hhhhccccccCCCCCEEEEecCCccCcHHH
Q psy3345         625 LSMGYGFVQFYTRESLNQALKVL-QNSSLDEHQIELKRSNRNLESEAT--TVKRKSSNVAKQTGSKILVRNIPFQAKQSE  701 (787)
Q Consensus       625 ~s~G~afV~F~~~e~A~~A~~~l-ng~~l~g~~l~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~V~nLp~~~t~~d  701 (787)
                      ..+|+++|+|.+.++|.+|+..+ ||..++| .+.+.++.........  ............+.++|||+|||+.+|+++
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~   89 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTE   89 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHH
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHH
Confidence            57899999999999999999999 9999999 9999988654331111  001112223345789999999999999999


Q ss_pred             HHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       702 L~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      |+++|++||.|.+|+|+++      ++|||||+|.+.++|.+|+..|| +..+.|++|+|+||.++.
T Consensus        90 l~~~F~~~G~i~~v~i~~~------~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           90 LERAFGYYGPLRSVWVARN------PPGFAFVEFEDPRDAADAVRELD-GRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHSCEEEEEECSS------SCSEEEEEESSHHHHHHHHHHHS-SSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHhhCCEEEEEEeeC------CCcEEEEEECCHHHHHHHHHHcC-CCEECCeEEEEEEcCCCC
Confidence            9999999999999999887      58999999999999999999997 699999999999998764

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.80  E-value=1.6e-19  Score=159.92  Aligned_cols=109  Identities=23%  Similarity=0.370  Sum_probs=75.1

Q ss_pred             CCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEE
Q psy3345         579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE  658 (787)
Q Consensus       579 ~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~  658 (787)
                      ..++|||+|||+++++++|+++|++||.|.+|+|+++..       .++|||||+|.+.++|.+|+..|||..|+|+.|.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-------~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~   76 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-------GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF   76 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-------EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-------CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            357899999999999999999999999999999998764       4899999999999999999999999999999999


Q ss_pred             EEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHH
Q psy3345         659 LKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS  700 (787)
Q Consensus       659 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~  700 (787)
                      |.++........      .........++|||+|||+.+|++
T Consensus        77 V~~a~~~~~~~~------~~~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           77 VGRFKSRKEREA------ELGARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             EEESSCCCC---------------------------------
T ss_pred             EEECCCcccccc------ccccccCCCCceEeCCCCCCcccc
Confidence            999876443111      111222345689999999999986

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.79  E-value=4.7e-19  Score=151.85  Aligned_cols=82  Identities=27%  Similarity=0.552  Sum_probs=77.9

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ..+++|||+|||..+|+++|+++|++||.|.+|+|+++. .+|+++|||||+|.++++|.+|++.|| +..+.|++|+|+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~kG~afV~f~~~~~A~~Ai~~ln-g~~~~gr~l~V~   94 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDK-VAGHSLGYGFVNYVTAKDAERAINTLN-GLRLQSKTIKVS   94 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECS-SSCCEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecC-CCCcccccEEEEECCHHHHHHHHHHhC-CCEECCEEEEEE
Confidence            467899999999999999999999999999999999985 689999999999999999999999997 799999999999


Q ss_pred             Eccc
Q psy3345         763 WAEE  766 (787)
Q Consensus       763 ~A~~  766 (787)
                      ||+|
T Consensus        95 ~AkP   98 (99)
T 4fxv_A           95 YARP   98 (99)
T ss_dssp             ECCB
T ss_pred             EeeC
Confidence            9987

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.78  E-value=9e-19  Score=165.17  Aligned_cols=137  Identities=24%  Similarity=0.342  Sum_probs=104.0

Q ss_pred             ccceEEEeecChHhHHHHHh-cCCcc-cCCeeEEEeecccCCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccC
Q psy3345         257 FLGMAYIGFKDEKNCNKALN-KNKSF-WKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIA  334 (787)
Q Consensus       257 ~~g~afV~F~~~~~A~~Al~-~~~~~-l~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  334 (787)
                      .+|+|||+|.+.++|++|+. +++.. +.|......   ......                   .+. ............
T Consensus        12 ~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~---~~~~~~-------------------~~~-~~~~~~~~~~~~   68 (158)
T 2kn4_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDD---ATKTFT-------------------VTE-GSHHHHHHMDVE   68 (158)
T ss_dssp             CEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEET---TTTEEE-------------------EEC-CCCCSSCCCCCC
T ss_pred             ccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccC---cccccc-------------------ccc-cccccccccCCC
Confidence            57999999999999999997 44322 333222210   000000                   000 000000111234


Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      ..++|||+|||+++|+++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus        69 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  148 (158)
T 2kn4_A           69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  148 (158)
T ss_dssp             BCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            56799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CC
Q psy3345         415 PK  416 (787)
Q Consensus       415 ~~  416 (787)
                      +.
T Consensus       149 ~~  150 (158)
T 2kn4_A          149 YG  150 (158)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.77  E-value=9.5e-19  Score=154.89  Aligned_cols=108  Identities=21%  Similarity=0.369  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP  415 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  415 (787)
                      ..+|||+|||+++|+++|+++|+.||.|.+|.|+.+.  +.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5689999999999999999999999999999999885  55899999999999999999999999999999999999886


Q ss_pred             CCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCCHH
Q psy3345         416 KENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPT  462 (787)
Q Consensus       416 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t~~  462 (787)
                      +.....                 .........++|||+|||+++|++
T Consensus        83 ~~~~~~-----------------~~~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           83 RKEREA-----------------ELGARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             CCC--------------------------------------------
T ss_pred             cccccc-----------------ccccccCCCCceEeCCCCCCcccc
Confidence            522110                 011123345679999999999875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.77  E-value=3.7e-19  Score=150.12  Aligned_cols=84  Identities=26%  Similarity=0.510  Sum_probs=77.9

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcC-CeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G-~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      +++|||+|||+.+|+++|+++|++|| .|.+|+|+++. .+|.++|||||+|.++++|.+||+.++|+..+.||+|.|+|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~-~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~   79 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNK-SSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHY   79 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCS-SSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecC-CCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEE
Confidence            36899999999999999999999999 89999999986 68999999999999999999999988767789999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      |.|+..
T Consensus        80 a~~~~~   85 (91)
T 2lxi_A           80 SDPKPK   85 (91)
T ss_dssp             CCSCCC
T ss_pred             cCCCCC
Confidence            998764

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.76  E-value=1.7e-18  Score=148.31  Aligned_cols=80  Identities=21%  Similarity=0.322  Sum_probs=76.4

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ..++|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.++++|.+|++.||+..|+||.|.
T Consensus        18 ~gt~lfV~n-----Lp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~   92 (99)
T 4fxv_A           18 QGTNLIVNY-----LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK   92 (99)
T ss_dssp             CCSEEEEES-----CCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            356799999     99999999999999999999999999988 699999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|+|
T Consensus        93 V~~AkP   98 (99)
T 4fxv_A           93 VSYARP   98 (99)
T ss_dssp             EEECCB
T ss_pred             EEEeeC
Confidence            999986

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=145.79  Aligned_cols=89  Identities=15%  Similarity=0.203  Sum_probs=81.5

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||+.+|+++|+++|++||.|.+|+|+++. .+|+++|||||+|.+.++|.+|++.|| +..+.|+.|.|+
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~-~tg~~rG~aFV~f~~~~~A~~Ai~~ln-g~~~~gr~i~V~   81 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHP-RTRKHLGLARVLFTSTRGAKETVKNLH-LTSVMGNIIHAQ   81 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCceeeEEEEEECCHHHHHHHHHHhC-CCEECCeEEEEE
Confidence            467899999999999999999999999999999999986 679999999999999999999999997 799999999999


Q ss_pred             EccccccHHHH
Q psy3345         763 WAEEADNVEDI  773 (787)
Q Consensus       763 ~A~~~~~~~~~  773 (787)
                      ||........+
T Consensus        82 ~a~~~~~~~~~   92 (110)
T 3s8s_A           82 LDIKGQQRMKY   92 (110)
T ss_dssp             ECSTTHHHHHH
T ss_pred             ECCCCcHHHHH
Confidence            99876654443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=145.79  Aligned_cols=82  Identities=15%  Similarity=0.192  Sum_probs=77.8

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..|...|+|.|     ||+++|+++|+++|+.||.|.+|+|++++ +|+++|||||.|.+.++|++||+.||+..|+||.
T Consensus         3 ~~p~~~lfV~n-----L~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~   77 (110)
T 3s8s_A            3 QIPLKEVTFAR-----LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNI   77 (110)
T ss_dssp             CSCCCEEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCcEEEEEC-----CCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            35677899999     99999999999999999999999999998 5999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|..
T Consensus        78 i~V~~a~~   85 (110)
T 3s8s_A           78 IHAQLDIK   85 (110)
T ss_dssp             CEEEECST
T ss_pred             EEEEECCC
Confidence            99999974

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.73  E-value=2.6e-18  Score=144.92  Aligned_cols=79  Identities=15%  Similarity=0.316  Sum_probs=74.0

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccC-ceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhc-cCccCCceE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKG-TVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFN-NTYVFSSRI   88 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~-~~~~~~~~i   88 (787)
                      |+.|+|+|     ||+++||+||+++|+.|| .|.+|+|++++ +|+++|||||.|.+.++|.+||+.++ +..|+||.|
T Consensus         1 S~~i~v~n-----Lp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i   75 (91)
T 2lxi_A            1 SNIVMLRM-----LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKV   75 (91)
T ss_dssp             CCEEEEET-----CCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEE
T ss_pred             CCEEEEeC-----CCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEE
Confidence            57899999     999999999999999999 89999999988 69999999999999999999999874 567999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.+|.+
T Consensus        76 ~V~~a~~   82 (91)
T 2lxi_A           76 SMHYSDP   82 (91)
T ss_dssp             EEECCCS
T ss_pred             EEEEcCC
Confidence            9999987

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.71  E-value=3.4e-17  Score=152.69  Aligned_cols=135  Identities=20%  Similarity=0.259  Sum_probs=109.3

Q ss_pred             CcEEEEEeCCHHHHHHHHHHh-cCCeeCCeeEEEEEecCccccccccccccccccccccccccchhhhhcccccccccCC
Q psy3345         483 GITGLVEFLQKNQAKAAFNSL-AYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQG  561 (787)
Q Consensus       483 ~~~a~V~F~~~~~A~~A~~~l-~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  561 (787)
                      .|+++|+|.+.++|++|+..+ +|..+.| ++.+.++............                               
T Consensus        13 ~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~-------------------------------   60 (150)
T 2i2y_A           13 KGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHH-------------------------------   60 (150)
T ss_dssp             CEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSS-------------------------------
T ss_pred             cccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccccc-------------------------------
Confidence            478999999999999999999 9999999 9999987543110000000                               


Q ss_pred             CcccccccccccccCCCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHH
Q psy3345         562 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN  641 (787)
Q Consensus       562 ~~~~~~~~~~~~~~~~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~  641 (787)
                            ...........+.++|||+|||+.+++++|+++|++||.|.+++++.+          ++|||||+|.+.++|.
T Consensus        61 ------~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----------~~g~afV~f~~~~~a~  124 (150)
T 2i2y_A           61 ------HHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----------PPGFAFVEFEDPRDAA  124 (150)
T ss_dssp             ------CCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----------SCSEEEEEESSHHHHH
T ss_pred             ------ccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----------CCcEEEEEECCHHHHH
Confidence                  000011223456789999999999999999999999999999999864          4699999999999999


Q ss_pred             HHHHHhCCCccCCeEEEEEecCcc
Q psy3345         642 QALKVLQNSSLDEHQIELKRSNRN  665 (787)
Q Consensus       642 ~A~~~lng~~l~g~~l~v~~~~~~  665 (787)
                      .|+..|||..++|+.|.|.++.+.
T Consensus       125 ~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A          125 DAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHcCCCEECCeEEEEEEcCCC
Confidence            999999999999999999998754

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.71  E-value=1.4e-17  Score=140.73  Aligned_cols=82  Identities=20%  Similarity=0.382  Sum_probs=74.8

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCC--eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCe----eecC
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGE--LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST----HLYG  756 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~--I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~----~~~G  756 (787)
                      ....+|||+|||+.+|+++|+++|++||.  |.+|+|++++ .+|++||||||+|.++++|.+|++.||+ .    .+.|
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~-~tg~srG~aFV~f~~~~~A~~Ai~~lng-~~~~~~i~G   84 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDK-QTQQNRGFAFVQLSSAMDASQLLQILQS-LHPPLKIDG   84 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCS-SSSSCSSEEEEECSSSHHHHHHHHHHHS-SSSCEEETT
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecC-CCCCCceEeEEEECCHHHHHHHHHHhcC-CCCCceECC
Confidence            45678999999999999999999999995  6789999986 6899999999999999999999999984 4    5899


Q ss_pred             ceEEEEEccc
Q psy3345         757 RRLVLEWAEE  766 (787)
Q Consensus       757 r~l~v~~A~~  766 (787)
                      |+|.|+||+.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999973

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.71  E-value=3.1e-17  Score=137.50  Aligned_cols=84  Identities=19%  Similarity=0.367  Sum_probs=76.2

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ||..+...|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..++|
T Consensus         1 Gp~~~~~~l~v~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   75 (87)
T 3bs9_A            1 GPLGSHFHVFVGD-----LSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG   75 (87)
T ss_dssp             -----CEEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCceEEEEeC-----CCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            5777888999999     99999999999999999999999999986 89999999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|++
T Consensus        76 ~~l~v~~a~~   85 (87)
T 3bs9_A           76 RQIRTNWATR   85 (87)
T ss_dssp             EECEEEEEC-
T ss_pred             eEEEEEecCC
Confidence            9999999986

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=7.5e-17  Score=138.77  Aligned_cols=86  Identities=15%  Similarity=0.225  Sum_probs=81.0

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      ++...++.+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+
T Consensus         2 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~   76 (99)
T 1whw_A            2 SSGSSGSGRLFVRN-----LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ   76 (99)
T ss_dssp             CCCCCSCEEEEEEC-----CCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESS
T ss_pred             CCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            44556788999999     99999999999999999999999999998 8999999999999999999999999999999


Q ss_pred             CceEEEEEccCC
Q psy3345          85 SSRIKVEKCSNL   96 (787)
Q Consensus        85 ~~~i~v~~~~~~   96 (787)
                      |+.|.|.++++.
T Consensus        77 g~~l~V~~a~~~   88 (99)
T 1whw_A           77 GRMLHVLPSTIK   88 (99)
T ss_dssp             SCEEEEEECCCC
T ss_pred             CcEEEEEEcCCC
Confidence            999999999973

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.70  E-value=7.1e-17  Score=133.95  Aligned_cols=82  Identities=26%  Similarity=0.511  Sum_probs=77.1

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      +++|||+|||..+|+++|+++|++||.|.+++++++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|+||
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~a~~a~~~l~-g~~~~g~~l~v~~a   78 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQNAMDSMQ-GQDLNGRPLRINWA   78 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECT-TTCCEEEEEEEEESCHHHHHHHHHHHT-TCEETTEECEEEEC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcC-CCCCccceEEEEECCHHHHHHHHHHhc-CCeeCCcEEEEEec
Confidence            3689999999999999999999999999999999885 689999999999999999999999997 79999999999999


Q ss_pred             cccc
Q psy3345         765 EEAD  768 (787)
Q Consensus       765 ~~~~  768 (787)
                      .+++
T Consensus        79 ~~~~   82 (83)
T 3md1_A           79 AKLE   82 (83)
T ss_dssp             CCCC
T ss_pred             CcCC
Confidence            9875

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.70  E-value=1.7e-17  Score=140.32  Aligned_cols=78  Identities=15%  Similarity=0.212  Sum_probs=72.7

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCc--eEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccC----ccCC
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGT--VTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNT----YVFS   85 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~--i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~----~~~~   85 (787)
                      +.|+|+|     ||+++|+++|+++|+.||.  |.+|+|++|+ +|+++|||||.|.+.++|++||+.||+.    .|+|
T Consensus        10 ~tlfV~n-----L~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A           10 DTIILRN-----IAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             CEEEEES-----CCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             CEEEEeC-----CCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            5699999     9999999999999999994  6799999988 6999999999999999999999999997    5999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      |.|.|.+|+.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999974

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.69  E-value=8.1e-17  Score=134.95  Aligned_cols=83  Identities=25%  Similarity=0.527  Sum_probs=75.6

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||..+|+++|+++|+.||.|.+++++.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v~   81 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDM-ATGKSKGYGFVSFFNKWDAENAIQQMG-GQWLGGRQIRTN   81 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC-CCCccceEEEEEECCHHHHHHHHHHcC-CCEECCeEEEEE
Confidence            467899999999999999999999999999999999885 589999999999999999999999997 699999999999


Q ss_pred             Ecccc
Q psy3345         763 WAEEA  767 (787)
Q Consensus       763 ~A~~~  767 (787)
                      ||+++
T Consensus        82 ~a~~k   86 (87)
T 3bs9_A           82 WATRK   86 (87)
T ss_dssp             EEC--
T ss_pred             ecCCC
Confidence            99864

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.69  E-value=1.5e-17  Score=151.39  Aligned_cols=124  Identities=18%  Similarity=0.247  Sum_probs=80.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHH
Q psy3345         628 GYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFK  707 (787)
Q Consensus       628 G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~  707 (787)
                      -++|++|.+...|..|+..++|....|+.- +.+..              ......+.++|||+|||..+|+++|+++|+
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~--------------~~~~~~~~~~l~V~nLp~~~te~~L~~~F~   69 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGR--------------PPPDVEGMTSLKVDNLTYRTSPDTLRRVFE   69 (135)
T ss_dssp             -------------------------------CCSCC--------------SCSSGGGCCCEEEECCCSSCHHHHHHHHHG
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcCC--------------CCCCCCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            367888899999999999998877666531 11111              112234578999999999999999999999


Q ss_pred             hcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         708 AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       708 ~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      .||.|..|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|+||++..
T Consensus        70 ~~G~i~~v~i~~~~-~~g~~~G~afV~F~~~~~A~~Ai~~l~-g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           70 KYGRVGDVYIPRDR-YTKESRGFAFVRFHDKRDAEDAMDAMD-GAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             GGSCCSEEECCCCS-SSSSCCSCCEEECSCHHHHHHHHTTTT-TCCSSSSCCEEEECCCCC
T ss_pred             hcCCEEEEEEEecC-CCCccceEEEEEECCHHHHHHHHHHcC-CCEECCEEEEEEECCCCC
Confidence            99999999999885 579999999999999999999999997 799999999999998654

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.69  E-value=6.1e-17  Score=135.04  Aligned_cols=83  Identities=24%  Similarity=0.399  Sum_probs=77.8

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ++..++..|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|
T Consensus         2 ~~~~~~~~l~V~n-----l~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   76 (85)
T 3mdf_A            2 SMATTKRVLYVGG-----LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG   76 (85)
T ss_dssp             -CCCCSSEEEEEC-----CCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCEEEEEC-----CCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4566788999999     99999999999999999999999999985 89999999999999999999999999999999


Q ss_pred             ceEEEEEcc
Q psy3345          86 SRIKVEKCS   94 (787)
Q Consensus        86 ~~i~v~~~~   94 (787)
                      +.|.|.+|+
T Consensus        77 ~~l~v~~ak   85 (85)
T 3mdf_A           77 RTIRVNLAK   85 (85)
T ss_dssp             EECEEEECC
T ss_pred             cEEEEEEcC
Confidence            999999885

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=5.1e-17  Score=138.44  Aligned_cols=80  Identities=19%  Similarity=0.345  Sum_probs=73.5

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-CeeecCceEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-STHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-~~~~~Gr~l~  760 (787)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|+++       ||||||+|.+.++|..|+..|++ +..+.|++|+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            457899999999999999999999999999999999875       79999999999999999999863 4789999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.++.
T Consensus        86 V~~A~~~~   93 (105)
T 1sjq_A           86 IQFSNHKE   93 (105)
T ss_dssp             BCCCSSSS
T ss_pred             EEEcCCCC
Confidence            99998665

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.69  E-value=3e-17  Score=141.24  Aligned_cols=85  Identities=25%  Similarity=0.384  Sum_probs=78.9

Q ss_pred             CCCEEEEecCCc------cCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC-
Q psy3345         684 TGSKILVRNIPF------QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG-  756 (787)
Q Consensus       684 ~~~~l~V~nLp~------~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G-  756 (787)
                      .+++|||.|||.      .+++++|+++|++||.|.+|+|+++. .+|+++|||||+|.++++|.+|+..|| +..+.| 
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~-~tg~~kG~afV~f~~~~~A~~Ai~~ln-g~~~~g~   82 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDE-ATGKTKGFLFVECGSMNDAKKIIKSFH-GKRLDLK   82 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEET-TTTEECSEEEEEESSHHHHHHHHHHHT-TCBSSSS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcC-CCCccceEEEEEECCHHHHHHHHHHhC-CcccCCC
Confidence            467899999999      99999999999999999999999985 679999999999999999999999997 799999 


Q ss_pred             ceEEEEEccccccH
Q psy3345         757 RRLVLEWAEEADNV  770 (787)
Q Consensus       757 r~l~v~~A~~~~~~  770 (787)
                      +.|.|.||.+.+..
T Consensus        83 r~l~V~~a~~~~~~   96 (100)
T 3ns6_A           83 HRLFLYTMKDVERY   96 (100)
T ss_dssp             CBCEEEESHHHHHH
T ss_pred             eEEEEEECchhhhh
Confidence            99999999876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1.5e-16  Score=137.09  Aligned_cols=84  Identities=23%  Similarity=0.363  Sum_probs=79.6

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .+..+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.+++|+++|||||.|.+.++|.+|++.||+..|+|+
T Consensus        12 ~~~~~~~~l~v~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   86 (100)
T 2do4_A           12 STSLEKHKLFISG-----LPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKEN   86 (100)
T ss_dssp             SSCCCCSCEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             ccCCCCCEEEEeC-----CCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            3445678899999     99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.++++
T Consensus        87 ~l~v~~a~~   95 (100)
T 2do4_A           87 IIKVAISNS   95 (100)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEECCC
Confidence            999999987

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.69  E-value=2.5e-17  Score=138.79  Aligned_cols=77  Identities=14%  Similarity=0.280  Sum_probs=70.6

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccC--ceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKG--TVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      .|+|.|     ||+++|+++|+++|+.||  .|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..|+||.|.|
T Consensus         3 ~l~V~n-----L~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V   77 (90)
T 3p5t_L            3 ALYIGN-----LTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV   77 (90)
T ss_dssp             -CEEES-----CCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEE
T ss_pred             EEEEeC-----CCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEE
Confidence            577777     999999999999999999  99999999997 8999999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      ..+.+
T Consensus        78 ~~~~~   82 (90)
T 3p5t_L           78 TPSNK   82 (90)
T ss_dssp             CCC--
T ss_pred             EECCC
Confidence            99987

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.68  E-value=2.1e-16  Score=134.99  Aligned_cols=86  Identities=17%  Similarity=0.343  Sum_probs=80.0

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      |+++|||+|||..+|+++|+++|+.||.|.+++|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|+.|.|+|
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~V~~   78 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP-QTGRSKGYAFIEFRDLESSASAVRNLN-GYQLGSRFLKCGY   78 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT-TTCCBCSEEEEEESSHHHHHHHHHHHT-TCEETTEECEEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-CCCccceEEEEEECCHHHHHHHHHHhC-CCeECCeEEEEEE
Confidence            46899999999999999999999999999999999885 579999999999999999999999997 7999999999999


Q ss_pred             ccccccHH
Q psy3345         764 AEEADNVE  771 (787)
Q Consensus       764 A~~~~~~~  771 (787)
                      |.+.....
T Consensus        79 a~~~~~~~   86 (96)
T 2x1f_A           79 SSNSDISG   86 (96)
T ss_dssp             CSCSSGGG
T ss_pred             cCCCCCCC
Confidence            99877543

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.1e-16  Score=136.72  Aligned_cols=84  Identities=19%  Similarity=0.268  Sum_probs=80.1

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHH----HHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      +|+|..+..+|+|.|     ||+.+|+++|+    ++|+.||.|.+|+|+.++.+  +|||||.|.+.++|++|++.||+
T Consensus         2 ss~~~~~~~~l~V~n-----L~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g   74 (96)
T 2dgx_A            2 SSGSSGNGADVQVSN-----IDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHR   74 (96)
T ss_dssp             CCCCCSSCEEEEEES-----CCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEEEC-----CCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCC
Confidence            577888889999999     99999999999    99999999999999998766  89999999999999999999999


Q ss_pred             CccCCceEEEEEccC
Q psy3345          81 TYVFSSRIKVEKCSN   95 (787)
Q Consensus        81 ~~~~~~~i~v~~~~~   95 (787)
                      ..|+||.|.|.+|++
T Consensus        75 ~~~~gr~l~V~~a~~   89 (96)
T 2dgx_A           75 YKIGSKKILVSLATG   89 (96)
T ss_dssp             EEETTEEEEEEECCC
T ss_pred             CEECCeEEEEEEcCC
Confidence            999999999999987

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=134.50  Aligned_cols=80  Identities=15%  Similarity=0.264  Sum_probs=72.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCee--ecCce
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH--LYGRR  758 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~--~~Gr~  758 (787)
                      ...|+++|||+|||+.+|+++|+++|++||.|.++++++.       ||||||+|.+.++|.+|+..|+ +..  +.||+
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-------kg~AFVef~~~~~A~~Av~~ln-~~~~~i~Gr~   88 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-------KRQALVEFEDVLGACNAVNYAA-DNQIYIAGHP   88 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHH-HSCEEETTEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-------CCEEEEEECCHHHHHHHHHHhc-CCCceeCCcE
Confidence            3457899999999999999999999999999999999764       7899999999999999999997 454  78999


Q ss_pred             EEEEEccccc
Q psy3345         759 LVLEWAEEAD  768 (787)
Q Consensus       759 l~v~~A~~~~  768 (787)
                      |+|+||+.++
T Consensus        89 i~V~~S~~k~   98 (100)
T 3r27_A           89 AFVNYSTSQK   98 (100)
T ss_dssp             EEEEECSCSC
T ss_pred             EEEEeccccc
Confidence            9999998764

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=6.6e-17  Score=139.27  Aligned_cols=82  Identities=12%  Similarity=0.172  Sum_probs=76.0

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .+..+...|+|.|     ||+++|++||+++|+.||.| +|+|+++++|+++|||||.|.+.++|++||+ +|+..|+||
T Consensus        10 ~~~~~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr   82 (102)
T 1wez_A           10 FQSTTGHCVHMRG-----LPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHR   82 (102)
T ss_dssp             CCCSSSCEEEEES-----CCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSS
T ss_pred             CCCCCCCEEEEeC-----CCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            4556677899999     99999999999999999954 9999999999999999999999999999996 699999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|+|..+.+
T Consensus        83 ~i~V~~~~~   91 (102)
T 1wez_A           83 YVELFLNST   91 (102)
T ss_dssp             CCEEEEECC
T ss_pred             EEEEEECCC
Confidence            999999886

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.68  E-value=1.5e-16  Score=132.64  Aligned_cols=82  Identities=24%  Similarity=0.482  Sum_probs=76.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|++||.|.+++++++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v   81 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMN-ESELFGRTIRV   81 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEET-TTTEECSEEEEEESSHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECC-CCCccccEEEEEECCHHHHHHHHHHhC-CCEECCcEEEE
Confidence            3467899999999999999999999999999999998885 688999999999999999999999997 79999999999


Q ss_pred             EEcc
Q psy3345         762 EWAE  765 (787)
Q Consensus       762 ~~A~  765 (787)
                      +||+
T Consensus        82 ~~ak   85 (85)
T 3mdf_A           82 NLAK   85 (85)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9985

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.3e-16  Score=134.58  Aligned_cols=83  Identities=18%  Similarity=0.346  Sum_probs=78.7

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +.++..|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus         2 ~~~~~~l~v~n-----lp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   76 (95)
T 2dnz_A            2 SSGSSGLYVGS-----LHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRP   76 (95)
T ss_dssp             CSCCCEEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCCcEEEEeC-----CCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcE
Confidence            45678899999     99999999999999999999999999987 6999999999999999999999999999999999


Q ss_pred             EEEEEccCC
Q psy3345          88 IKVEKCSNL   96 (787)
Q Consensus        88 i~v~~~~~~   96 (787)
                      |.|.++++.
T Consensus        77 l~V~~a~~~   85 (95)
T 2dnz_A           77 MRVGHVTER   85 (95)
T ss_dssp             CEEEESSCC
T ss_pred             EEEEEcccc
Confidence            999999873

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=1.7e-16  Score=136.42  Aligned_cols=86  Identities=22%  Similarity=0.308  Sum_probs=79.9

Q ss_pred             CCCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEE--------EEEEecC-CCCcceEEEEEecCHHHHHHH
Q psy3345           4 HLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD--------VQLKYTT-EGKFRRFAFIGYHREDQAQAA   74 (787)
Q Consensus         4 ~~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~-~g~~~g~afv~f~~~~~a~~a   74 (787)
                      ....|..+...|+|.|     ||+++|+++|+++|+.||.|..        |+|+.++ +|+++|||||.|.+.++|++|
T Consensus         5 ~~~~~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~A   79 (99)
T 2la6_A            5 HHHHSHSDNNTIFVQG-----LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAA   79 (99)
T ss_dssp             CSCCSCCCCSEEEEEC-----CCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHH
T ss_pred             CCCCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHH
Confidence            4455666788899999     9999999999999999999999        9999987 799999999999999999999


Q ss_pred             HHHhccCccCCceEEEEEcc
Q psy3345          75 LDYFNNTYVFSSRIKVEKCS   94 (787)
Q Consensus        75 ~~~~~~~~~~~~~i~v~~~~   94 (787)
                      ++.||+..|+||.|.|.+|+
T Consensus        80 i~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           80 IDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HHHHTTCBSSSSBCEEEECC
T ss_pred             HHHhCCCEeCCcEEEEEecC
Confidence            99999999999999999884

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=9.8e-17  Score=139.28  Aligned_cols=76  Identities=13%  Similarity=0.185  Sum_probs=72.5

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      ..|+|+|     |||++|++||++||+.| .|.+|+|+++++|+++|||||.|.+.++|.+|| .+|+..|+||+|+|..
T Consensus        17 ~~v~V~n-----Lp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   89 (109)
T 2dnn_A           17 LYVSVHG-----MPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSP   89 (109)
T ss_dssp             HEEEEEC-----CCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEE
T ss_pred             CEEEEeC-----CCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            4699999     99999999999999999 799999999999999999999999999999999 5799999999999999


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      |.+
T Consensus        90 a~~   92 (109)
T 2dnn_A           90 ATE   92 (109)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            875

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.68  E-value=1.2e-16  Score=151.31  Aligned_cols=136  Identities=20%  Similarity=0.326  Sum_probs=79.9

Q ss_pred             EEeCCHHHHHHHHHHhCCCccC--CeEEEEEecCccccch--h----hhhhhccccccCCCCCEEEEecCCccCcHHHHH
Q psy3345         632 VQFYTRESLNQALKVLQNSSLD--EHQIELKRSNRNLESE--A----TTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVE  703 (787)
Q Consensus       632 V~F~~~e~A~~A~~~lng~~l~--g~~l~v~~~~~~~~~~--~----~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~  703 (787)
                      .+|.+.++|..|+..+++....  |+.+....+.+.....  .    ......+.+....+.++|||.|||..+|+++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6789999999999999887665  6666655533221100  0    000012223334567899999999999999999


Q ss_pred             HHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccccc
Q psy3345         704 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       704 ~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~  769 (787)
                      ++|+.||.|..|.|+.+. .+|.++|||||+|.+.++|..||..|| +..|.|+.|.|.||.++..
T Consensus        91 ~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAAKEALN-GAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHHGGGSCEEEEEEEECT-TTSSEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECEEEESEECC-
T ss_pred             HHhhcCCCEEEEEEEecC-CCCcEeeEEEEEECCHHHHHHHHHHhC-CCEECCEEEEEEEecCCCC
Confidence            999999999999999885 689999999999999999999999997 7999999999999987664

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.6e-16  Score=128.49  Aligned_cols=75  Identities=23%  Similarity=0.281  Sum_probs=70.2

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      .+..|+|+||++.+|+++|+++|.+||.|.++++..       ++|||||+|.++++|.+|++.|| +..++||.|+|++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-------~kGfaFVey~~~~eA~~Ai~~Ln-~~~l~gr~I~V~~   77 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-------NQGIALCKYTTREEANKAQMALN-NCVLANTTIFAES   77 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHT-TEEETTEEEEEEC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-------CCcEEEEEECCHHHHHHHHHHhc-CCEECCcEEEEEE
Confidence            467899999999999999999999999999999855       58999999999999999999997 6999999999999


Q ss_pred             ccc
Q psy3345         764 AEE  766 (787)
Q Consensus       764 A~~  766 (787)
                      |.+
T Consensus        78 A~e   80 (89)
T 2wbr_A           78 PSE   80 (89)
T ss_dssp             CCH
T ss_pred             CCH
Confidence            953

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.5e-16  Score=135.39  Aligned_cols=85  Identities=22%  Similarity=0.306  Sum_probs=78.7

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ++++..++..|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|
T Consensus         9 ~~~~~~~~~~l~V~n-----lp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   83 (94)
T 2e5h_A            9 SGGLAPSKSTVYVSN-----LPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQL   83 (94)
T ss_dssp             CCSCCCCTTSEEEES-----CCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEE
T ss_pred             CCCCCCCCCEEEEEC-----CCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCee
Confidence            344556778899999     99999999999999999999999999987 589999999999999999999999999999


Q ss_pred             CCceEEEEEcc
Q psy3345          84 FSSRIKVEKCS   94 (787)
Q Consensus        84 ~~~~i~v~~~~   94 (787)
                      .|+.|.|.+|+
T Consensus        84 ~g~~l~v~~ak   94 (94)
T 2e5h_A           84 FGRVIKASIAI   94 (94)
T ss_dssp             TTEEEEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999985

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.67  E-value=2.2e-16  Score=137.79  Aligned_cols=84  Identities=20%  Similarity=0.355  Sum_probs=78.8

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .+..++.+|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|
T Consensus        21 ~~~~~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g   95 (108)
T 2jrs_A           21 KGSAGPMRLYVGS-----LHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG   95 (108)
T ss_dssp             CSCSSCEEEEEEC-----CCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             cCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3445677899999     99999999999999999999999999986 79999999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|++
T Consensus        96 ~~l~V~~a~~  105 (108)
T 2jrs_A           96 RPMKVGHVTE  105 (108)
T ss_dssp             SCCEEECSCS
T ss_pred             EEEEEEEccc
Confidence            9999999987

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=2.9e-16  Score=135.05  Aligned_cols=86  Identities=23%  Similarity=0.417  Sum_probs=80.2

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~V   82 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS-LTKKPKGFAFVTFMFPEHAVKAYAEVD-GQVFQGRMLHV   82 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT-TTCCCCSEEEEEESSHHHHHHHHHHTT-TEESSSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC-CCCCcCeEEEEEECCHHHHHHHHHHhC-CCEECCcEEEE
Confidence            3467899999999999999999999999999999999985 589999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus        83 ~~a~~~~~   90 (99)
T 1whw_A           83 LPSTIKKE   90 (99)
T ss_dssp             EECCCCST
T ss_pred             EEcCCCcc
Confidence            99998765

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3e-16  Score=134.98  Aligned_cols=85  Identities=19%  Similarity=0.336  Sum_probs=79.5

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ++.+..+..+|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++ ||+..|
T Consensus         3 ~~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~   76 (99)
T 2dgs_A            3 SGSSGSKSNKIFVGG-----IPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDI   76 (99)
T ss_dssp             CCCCCSSCCEEEEES-----CCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBS
T ss_pred             CCCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEE
Confidence            345556788899999     99999999999999999999999999987 69999999999999999999999 899999


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +|+.|.|.++.+
T Consensus        77 ~g~~l~V~~a~~   88 (99)
T 2dgs_A           77 MGKKVEVKRAEP   88 (99)
T ss_dssp             SSCBCEEEECCC
T ss_pred             CCeEEEEEECCC
Confidence            999999999987

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.9e-16  Score=137.12  Aligned_cols=86  Identities=19%  Similarity=0.335  Sum_probs=80.9

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      +++...+...|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..|
T Consensus         5 ~~~~~~~~~~l~v~n-----Lp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   79 (102)
T 1x5s_A            5 SSGMASDEGKLFVGG-----LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV   79 (102)
T ss_dssp             CCCCCCCCSEEEEES-----CCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCT
T ss_pred             CCCCCCCCCEEEEEC-----CCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEE
Confidence            455666788999999     99999999999999999999999999987 789999999999999999999999999999


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +|+.|.|.+|++
T Consensus        80 ~g~~l~v~~a~~   91 (102)
T 1x5s_A           80 DGRQIRVDQAGK   91 (102)
T ss_dssp             TSCCCEEEEEEC
T ss_pred             CCeEEEEEECCC
Confidence            999999999997

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.7e-16  Score=134.16  Aligned_cols=85  Identities=24%  Similarity=0.360  Sum_probs=79.1

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      ..+..++..|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+
T Consensus         9 ~~~~~~~~~l~v~n-----lp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   83 (95)
T 2cqc_A            9 RANPDPNCCLGVFG-----LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD   83 (95)
T ss_dssp             CCSCCGGGCEEEES-----CCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             CCCCCCCCEEEEEC-----CCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            34456778899999     99999999999999999999999999987 5899999999999999999999999999999


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      |+.|.|.+|+.
T Consensus        84 g~~l~v~~a~~   94 (95)
T 2cqc_A           84 GRRIRVSGPSS   94 (95)
T ss_dssp             TEEEEEECCSC
T ss_pred             CEEEEEEecCC
Confidence            99999999874

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.7e-16  Score=134.16  Aligned_cols=85  Identities=25%  Similarity=0.470  Sum_probs=79.3

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||.|||..+|+++|+++|++||.|.+++++++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|+|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~V~   80 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDS-DTGRSKGYGFITFSDSECARRALEQLN-GFELAGRPMRVG   80 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCS-SSCCCCSEEEEEESCHHHHHHHHHHHT-TCCSSSSCCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecC-CCCceeeEEEEEECCHHHHHHHHHHhC-CCeeCCcEEEEE
Confidence            467899999999999999999999999999999999986 579999999999999999999999997 799999999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||.++..
T Consensus        81 ~a~~~~~   87 (95)
T 2dnz_A           81 HVTERLD   87 (95)
T ss_dssp             ESSCCCC
T ss_pred             EcccccC
Confidence            9987654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=3.2e-16  Score=135.03  Aligned_cols=85  Identities=21%  Similarity=0.414  Sum_probs=79.3

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||+|||..+|+++|+++|+.||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   89 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR--AGKPKGLAYVEYENESQASQAVMKMD-GMTIKENIIK   89 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT--TSCEEEEEEEEESSHHHHHHHHHHHT-TEESSSCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC--CCCEEeEEEEEECCHHHHHHHHHHhC-CCEECCEEEE
Confidence            34567899999999999999999999999999999999984  89999999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.+..
T Consensus        90 v~~a~~~~   97 (100)
T 2do4_A           90 VAISNSGP   97 (100)
T ss_dssp             EEECCCCS
T ss_pred             EEECCCCC
Confidence            99999765

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.7e-16  Score=136.59  Aligned_cols=86  Identities=14%  Similarity=0.177  Sum_probs=82.1

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceE-EEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVT-DVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTY   82 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~-~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~   82 (787)
                      ++++..++.+|+|.|     ||+++|+++|+++|+.||.|. +|+|+.++ +|+++|||||.|.+.++|++|++.||+..
T Consensus         2 ss~~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   76 (99)
T 2div_A            2 SSGSSGMAASLWMGD-----LEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKP   76 (99)
T ss_dssp             CCCCCSSSSEEEECS-----CCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSE
T ss_pred             CCCCCCCccEEEEeC-----CCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCc
Confidence            567778899999999     999999999999999999999 99999997 79999999999999999999999999999


Q ss_pred             cCCce----EEEEEccC
Q psy3345          83 VFSSR----IKVEKCSN   95 (787)
Q Consensus        83 ~~~~~----i~v~~~~~   95 (787)
                      |.|+.    |.|.+|++
T Consensus        77 ~~g~~~~~~l~v~~a~~   93 (99)
T 2div_A           77 LPGATPAKRFKLNYATY   93 (99)
T ss_dssp             ESSCSSCEECCEEETTC
T ss_pred             cCCCCcceeEEEeecCC
Confidence            99999    99999987

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.67  E-value=7.1e-17  Score=138.83  Aligned_cols=83  Identities=16%  Similarity=0.265  Sum_probs=78.3

Q ss_pred             CCcccceEEEecCcccCCCc------cCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345           8 PVVPRNHISLLDLDEVEFIY------KITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~------~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      +...++.|+|.|     ||+      ++|+++|+++|+.||.|.+|+|++++ +|+++|||||.|.++++|.+||+.||+
T Consensus         2 ~~~~~~~vfV~n-----Lp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng   76 (100)
T 3ns6_A            2 PLGSDQYIVVNG-----APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG   76 (100)
T ss_dssp             CSCGGGEEEEES-----CCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCcCcEEEEeC-----CCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            445577899999     999      99999999999999999999999998 499999999999999999999999999


Q ss_pred             CccCC-ceEEEEEccC
Q psy3345          81 TYVFS-SRIKVEKCSN   95 (787)
Q Consensus        81 ~~~~~-~~i~v~~~~~   95 (787)
                      ..|+| |.|.|.+|.+
T Consensus        77 ~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           77 KRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             CBSSSSCBCEEEESHH
T ss_pred             cccCCCeEEEEEECch
Confidence            99999 9999999986

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.67  E-value=2.1e-16  Score=134.82  Aligned_cols=83  Identities=19%  Similarity=0.309  Sum_probs=78.1

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +..+...|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.+++|+++|||||.|.+.++|.+|++.||+..|.|+.
T Consensus        12 ~~~~~~~l~v~n-----lp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (95)
T 2ywk_A           12 QEEADRTVFVGN-----LEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRP   86 (95)
T ss_dssp             CTTGGGEEEEEC-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEEC-----CCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCE
Confidence            344677899999     999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|+.
T Consensus        87 l~V~~a~~   94 (95)
T 2ywk_A           87 INVSGPSS   94 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999863

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.3e-16  Score=128.90  Aligned_cols=79  Identities=16%  Similarity=0.161  Sum_probs=72.9

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ++.-.+.-|.|+|     |++.+||++|+++|..||+|.+++|..     ++|||||.|.++++|.+|++.||+..+.||
T Consensus         2 ~~~~~~~wL~VgN-----L~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr   71 (89)
T 2wbr_A            2 AMAWGSSWLLLKN-----LTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANT   71 (89)
T ss_dssp             CCCCCCCEEEEEC-----CCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCccceEEEeC-----CCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCc
Confidence            3444578899999     999999999999999999999999976     589999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|.+
T Consensus        72 ~I~V~~A~e   80 (89)
T 2wbr_A           72 TIFAESPSE   80 (89)
T ss_dssp             EEEEECCCH
T ss_pred             EEEEEECCH
Confidence            999999864

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.1e-16  Score=132.50  Aligned_cols=82  Identities=13%  Similarity=0.252  Sum_probs=77.5

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .+......|+|.|     ||+++|++||+++|+.| .|.+|+|+.+.+|+++|||||.|.+.++|++||+ ||+..|+||
T Consensus         5 ~~~~~~~~l~v~n-----Lp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr   77 (91)
T 2dgw_A            5 SSGTTCHTVKLRG-----APFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGR   77 (91)
T ss_dssp             CCCCCCCEEEEEC-----CCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTE
T ss_pred             CCCCCccEEEEEC-----CCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCc
Confidence            4455678899999     99999999999999999 8999999999899999999999999999999999 999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|.+
T Consensus        78 ~i~v~~a~~   86 (91)
T 2dgw_A           78 YIEVFREKS   86 (91)
T ss_dssp             EEEEEEESS
T ss_pred             EEEEEECCc
Confidence            999999987

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.67  E-value=2e-16  Score=137.96  Aligned_cols=87  Identities=22%  Similarity=0.457  Sum_probs=80.3

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||+|||..+|+++|+++|++||.|.+|+|+++. .+|+++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~F~~~~~A~~Ai~~l~-g~~i~g~~l~   99 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS-ETGRSKGYGFITFSDSECAKKALEQLN-GFELAGRPMK   99 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEET-TTTEEEEEEEEEESCHHHHHHHHHHHT-TCCSSSSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCccceEEEEEECCHHHHHHHHHHcC-CCEECCEEEE
Confidence            34567899999999999999999999999999999999885 578999999999999999999999997 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.++.+
T Consensus       100 V~~a~~k~d  108 (108)
T 2jrs_A          100 VGHVTERTD  108 (108)
T ss_dssp             EECSCSSCC
T ss_pred             EEEcccCCC
Confidence            999998753

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.66  E-value=9.2e-17  Score=145.23  Aligned_cols=80  Identities=20%  Similarity=0.208  Sum_probs=75.8

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCc---eEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGT---VTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ....+|+|.|     |||++|++||+++|+.||.   |.+|+|+++++|+++|||||.|.+.++|++||+ +|+..|+||
T Consensus        42 ~~~~~lfVgn-----Lp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr  115 (136)
T 2hgl_A           42 GEGFVVKLRG-----LPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHR  115 (136)
T ss_dssp             CTTCEEEEES-----CCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSS
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCE
Confidence            3567799999     9999999999999999998   899999999999999999999999999999999 899999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|+|..|.+
T Consensus       116 ~i~V~~a~~  124 (136)
T 2hgl_A          116 YIEVFKSHR  124 (136)
T ss_dssp             EEEEEECCH
T ss_pred             EEEEEECCh
Confidence            999999875

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.66  E-value=2.9e-16  Score=130.20  Aligned_cols=78  Identities=15%  Similarity=0.321  Sum_probs=74.5

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      .+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..++|+.|.|.
T Consensus         2 ~~l~V~n-----lp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   76 (83)
T 3md1_A            2 FNLFVGD-----LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN   76 (83)
T ss_dssp             EEEEEEC-----CCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             eEEEEeC-----CCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            4688888     99999999999999999999999999986 79999999999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +|++
T Consensus        77 ~a~~   80 (83)
T 3md1_A           77 WAAK   80 (83)
T ss_dssp             ECCC
T ss_pred             ecCc
Confidence            9986

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.66  E-value=1.9e-16  Score=135.28  Aligned_cols=80  Identities=23%  Similarity=0.350  Sum_probs=76.9

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      |+..|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|+.|.
T Consensus         1 P~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   75 (96)
T 2x1f_A            1 PSRVVYLGS-----IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLK   75 (96)
T ss_dssp             CCSEEEEES-----CCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCcEEEEEC-----CCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            577899999     99999999999999999999999999987 699999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|.+
T Consensus        76 V~~a~~   81 (96)
T 2x1f_A           76 CGYSSN   81 (96)
T ss_dssp             EEECSC
T ss_pred             EEEcCC
Confidence            999987

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.8e-16  Score=134.29  Aligned_cols=85  Identities=27%  Similarity=0.487  Sum_probs=78.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+. |+ +..+.|++|.|
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~-~~-~~~~~g~~l~V   83 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA-EKQRPRGFGFITFEDEQSVDQAVN-MH-FHDIMGKKVEV   83 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCT-TTCSCCSEEEEEESSHHHHHHHHH-HC-CCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-CCCCCCceEEEEECCHHHHHHHHH-hC-CCEECCeEEEE
Confidence            4577999999999999999999999999999999999885 679999999999999999999999 86 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      .||.++..
T Consensus        84 ~~a~~~~~   91 (99)
T 2dgs_A           84 KRAEPRDS   91 (99)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCcc
Confidence            99997764

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.66  E-value=2.1e-16  Score=140.06  Aligned_cols=105  Identities=22%  Similarity=0.359  Sum_probs=94.4

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ  656 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~  656 (787)
                      +.+.++|||+|||+.+++++|+++|++||.|.++.++.+.        .++|||||+|.+.++|.+|+..|||..++|+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--------~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   76 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--------ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRY   76 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST--------TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC--------CCCcEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            4567899999999999999999999999999999998753        36899999999999999999999999999999


Q ss_pred             EEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCC
Q psy3345         657 IELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGE  711 (787)
Q Consensus       657 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~  711 (787)
                      |.|.++.....                      -++++...++++|.++|++||.
T Consensus        77 l~v~~a~~~~~----------------------~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           77 LVVLYYNANRA----------------------FQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CEEEECCHHHH----------------------TTTSCHHHHHHHHHHHHHHHCC
T ss_pred             EEEEEecCChh----------------------hhhhhHhHhHHHHHHHHHHhCC
Confidence            99999875444                      0578899999999999999993

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.4e-16  Score=138.10  Aligned_cols=82  Identities=17%  Similarity=0.235  Sum_probs=76.7

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEE-EEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      +..+..+|+|.|     ||+++|++||+++|+.||.|.+ |+|+++.+|+++|||||.|.++++|++||+. |+..|+||
T Consensus        11 ~~~~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr   84 (104)
T 1wg5_A           11 DTANDGFVRLRG-----LPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHR   84 (104)
T ss_dssp             SCSCCCEEEEES-----CCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSS
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCc
Confidence            345678899999     9999999999999999999987 9999998999999999999999999999999 99999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      +|+|..+.+
T Consensus        85 ~i~v~~~~~   93 (104)
T 1wg5_A           85 YIEIFKSSR   93 (104)
T ss_dssp             CCEEEEECT
T ss_pred             EEEEEECCH
Confidence            999999876

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.66  E-value=3.2e-16  Score=132.80  Aligned_cols=84  Identities=23%  Similarity=0.267  Sum_probs=79.5

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      +++..+..+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+ +|+++|||||.|.+.++|.+|++.||+..|+|
T Consensus         2 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g   75 (92)
T 2dgv_A            2 SSGSSGACQIFVRN-----LPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSG   75 (92)
T ss_dssp             CCSSSSCCEEEECS-----CCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTT
T ss_pred             CCCCCCCcEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            45667788999999     9999999999999999999999999984 89999999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus        76 ~~l~v~~a~~   85 (92)
T 2dgv_A           76 REIDVRIDRN   85 (92)
T ss_dssp             BCCCCEECSC
T ss_pred             cEEEEEEcCC
Confidence            9999999987

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.3e-16  Score=133.29  Aligned_cols=83  Identities=23%  Similarity=0.467  Sum_probs=77.4

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|.+++|+.+. .+|.++|||||+|.+.++|.+|++.|| +..+.|++|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~   89 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK-DTRKSKGVAFILFLDKDSAQNCTRAIN-NKQLFGRVIK   89 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCS-SSCCCTTCEEEEESCHHHHHHHHHHTT-TEEETTEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-CCCCcccEEEEEECCHHHHHHHHHHcC-CCeeCCcEEE
Confidence            34567899999999999999999999999999999999986 578999999999999999999999997 7999999999


Q ss_pred             EEEcc
Q psy3345         761 LEWAE  765 (787)
Q Consensus       761 v~~A~  765 (787)
                      |+||+
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99985

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.66  E-value=8.9e-16  Score=136.01  Aligned_cols=84  Identities=19%  Similarity=0.330  Sum_probs=78.8

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ...+...|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|++||+.||+..|+|+
T Consensus        11 ~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (115)
T 2dgo_A           11 DTSNHFHVFVGD-----LSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR   85 (115)
T ss_dssp             CSTTCEEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCCcEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            344667799999     99999999999999999999999999987 899999999999999999999999999999999


Q ss_pred             eEEEEEccCC
Q psy3345          87 RIKVEKCSNL   96 (787)
Q Consensus        87 ~i~v~~~~~~   96 (787)
                      .|.|.+|++.
T Consensus        86 ~l~V~~a~~~   95 (115)
T 2dgo_A           86 QIRTNWATRK   95 (115)
T ss_dssp             ECEEEESSCC
T ss_pred             EEEEEEccCC
Confidence            9999999973

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.3e-16  Score=136.51  Aligned_cols=87  Identities=25%  Similarity=0.396  Sum_probs=81.4

Q ss_pred             CCCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCc
Q psy3345           4 HLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTY   82 (787)
Q Consensus         4 ~~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~   82 (787)
                      .+++...+...|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..
T Consensus         4 ~~~~~~~~~~~l~V~n-----Lp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~   78 (102)
T 2cqb_A            4 GSSGMATTKRVLYVGG-----LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE   78 (102)
T ss_dssp             CSSCSCCCCSCEEEES-----CCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEE
T ss_pred             CcCCcCCCCCEEEEeC-----CCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            3455666888999999     99999999999999999999999999986 79999999999999999999999999999


Q ss_pred             cCCceEEEEEccC
Q psy3345          83 VFSSRIKVEKCSN   95 (787)
Q Consensus        83 ~~~~~i~v~~~~~   95 (787)
                      |+|+.|.|.++++
T Consensus        79 ~~g~~l~V~~a~~   91 (102)
T 2cqb_A           79 LFGRTIRVNLAKP   91 (102)
T ss_dssp             ETTEEEEEEECCC
T ss_pred             ECCcEEEEEeCCC
Confidence            9999999999987

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.8e-16  Score=136.21  Aligned_cols=81  Identities=22%  Similarity=0.385  Sum_probs=76.8

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .++..|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|+.|
T Consensus        21 ~~~~~l~V~n-----lp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   95 (106)
T 1p27_B           21 VEGWILFVTG-----VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   95 (106)
T ss_dssp             TTBEEEEEEC-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            3456799999     99999999999999999999999999987 69999999999999999999999999999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.+|.+
T Consensus        96 ~V~~a~~  102 (106)
T 1p27_B           96 SVDWCFV  102 (106)
T ss_dssp             EEEESEE
T ss_pred             EEEeecC
Confidence            9999987

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.8e-16  Score=136.48  Aligned_cols=81  Identities=16%  Similarity=0.234  Sum_probs=76.4

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      ..+...|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+++|+++|||||+|.+.++|.+||. +|+..|+||.|
T Consensus         8 ~~~~~~lfV~~-----Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l   81 (103)
T 1s79_A            8 DVKNRSVYIKG-----FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDL   81 (103)
T ss_dssp             CSGGGCEEEEC-----CCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTC
T ss_pred             cCCCCEEEEEC-----CCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEE
Confidence            34567899999     9999999999999999999999999999899999999999999999999999 79999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.++..
T Consensus        82 ~V~~~~~   88 (103)
T 1s79_A           82 LILFKDD   88 (103)
T ss_dssp             EEEEHHH
T ss_pred             EEEEchH
Confidence            9998875

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.4e-16  Score=135.52  Aligned_cols=86  Identities=16%  Similarity=0.277  Sum_probs=80.5

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ......+..+|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|
T Consensus         8 ~~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   82 (105)
T 1x5u_A            8 PISERNQDATVYVGG-----LDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL   82 (105)
T ss_dssp             CCCCCCTTTEEEEEC-----CCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBC
T ss_pred             CcccCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeE
Confidence            344555778899999     99999999999999999999999999988 799999999999999999999999999999


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +|+.|.|.+|.+
T Consensus        83 ~g~~l~v~~a~~   94 (105)
T 1x5u_A           83 YGKPIRVNKASA   94 (105)
T ss_dssp             SSCBCEEEETTT
T ss_pred             CCeEEEEEECCC
Confidence            999999999987

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=6.6e-16  Score=133.86  Aligned_cols=84  Identities=18%  Similarity=0.268  Sum_probs=79.3

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ..+..+..+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+ +|+++|||||.|.+.++|.+|++.||+..|.|
T Consensus         9 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   82 (103)
T 2d9p_A            9 RITRYQVVNLYVKN-----LDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT   82 (103)
T ss_dssp             CCCCSSCCCEEEEC-----CCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             ccCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            34455788899999     9999999999999999999999999998 89999999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|++
T Consensus        83 ~~l~V~~a~~   92 (103)
T 2d9p_A           83 KPLYVALAQR   92 (103)
T ss_dssp             SBCEEEECSS
T ss_pred             cEEEEEEecc
Confidence            9999999997

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4e-16  Score=133.09  Aligned_cols=84  Identities=23%  Similarity=0.335  Sum_probs=78.0

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|.+++|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~   88 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-QSRRSRGFAFVYFENVDDAKEAKERAN-GMELDGRRIR   88 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECS-SSSSEEEEEEEEESSHHHHHHHHHHHT-TEEETTEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcC-CCCCcccEEEEEECCHHHHHHHHHHhC-CCEECCEEEE
Confidence            34567899999999999999999999999999999999885 578999999999999999999999997 7999999999


Q ss_pred             EEEccc
Q psy3345         761 LEWAEE  766 (787)
Q Consensus       761 v~~A~~  766 (787)
                      |+||+.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999974

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.2e-16  Score=135.70  Aligned_cols=87  Identities=25%  Similarity=0.476  Sum_probs=80.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|..|+|+.+. .+|.++|||||+|.+.++|.+|+..|+ +..+.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   88 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-VTGQHQGYGFVEFLSEEDADYAIKIMD-MIKLYGKPIR   88 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCSBCSCEEEEESSHHHHHHHHHHSS-SCBCSSCBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCcCCcEEEEEECCHHHHHHHHHHhC-CCeECCeEEE
Confidence            34578999999999999999999999999999999999985 589999999999999999999999997 6999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |.||.++..
T Consensus        89 v~~a~~~~~   97 (105)
T 1x5u_A           89 VNKASAHNK   97 (105)
T ss_dssp             EEETTTTSC
T ss_pred             EEECCCCCc
Confidence            999987654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.66  E-value=1.5e-16  Score=141.28  Aligned_cols=80  Identities=21%  Similarity=0.233  Sum_probs=75.5

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCc---eEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGT---VTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .....|+|.|     ||+++|++||++||+.||.   |.+|+|+++++|+++|||||.|.+.++|.+||+ +|+..|+||
T Consensus        15 ~~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   88 (118)
T 2db1_A           15 GEGYVVKLRG-----LPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHR   88 (118)
T ss_dssp             CCCCEEEEES-----CCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCcEEEEeC-----CCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCe
Confidence            3456799999     9999999999999999998   899999999999999999999999999999999 899999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|+|..|.+
T Consensus        89 ~i~V~~a~~   97 (118)
T 2db1_A           89 YIEVFKSHR   97 (118)
T ss_dssp             EEEEEEECH
T ss_pred             EEEEEECCH
Confidence            999999875

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=1.8e-16  Score=135.19  Aligned_cols=81  Identities=14%  Similarity=0.245  Sum_probs=72.9

Q ss_pred             CCCCCEEEEecCCc-cCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-CeeecCceE
Q psy3345         682 KQTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-STHLYGRRL  759 (787)
Q Consensus       682 ~~~~~~l~V~nLp~-~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-~~~~~Gr~l  759 (787)
                      ..++++|||+|||+ .+|+++|+++|++||.|.+|+|+++       +|||||+|.+.++|..|+..||+ +..+.||+|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            45789999999999 9999999999999999999999876       58999999999999999999973 246999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      +|+||++...
T Consensus        85 ~V~~a~~~~~   94 (102)
T 1x4d_A           85 RVHLSQKYKR   94 (102)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEECCCCCC
Confidence            9999996554

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=5.3e-16  Score=135.57  Aligned_cols=89  Identities=73%  Similarity=1.177  Sum_probs=80.7

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+++...+|.++|||||+|.+.++|.+|+..|+|+..+.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            34578999999999999999999999999999999999872158999999999999999999999999337999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.++..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999997765

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.65  E-value=5.6e-16  Score=137.27  Aligned_cols=82  Identities=18%  Similarity=0.221  Sum_probs=78.0

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+||+.||+..|+|+.|
T Consensus        23 ~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   97 (115)
T 2cpz_A           23 PEGANLFIYH-----LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   97 (115)
T ss_dssp             STTCCEEEES-----CCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCcEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            4567899999     99999999999999999999999999998 79999999999999999999999999999999999


Q ss_pred             EEEEccCC
Q psy3345          89 KVEKCSNL   96 (787)
Q Consensus        89 ~v~~~~~~   96 (787)
                      .|.++++.
T Consensus        98 ~V~~a~~~  105 (115)
T 2cpz_A           98 KVQLKRSK  105 (115)
T ss_dssp             EEECCCCS
T ss_pred             EEEEcCCC
Confidence            99999873

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.7e-16  Score=135.23  Aligned_cols=86  Identities=23%  Similarity=0.443  Sum_probs=79.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~V   86 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMN-ESELFGRTIRV   86 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCS-SSCCCSSEEEECCSSHHHHHHHHHHHT-TEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecC-CCCCcceEEEEEECCHHHHHHHHHHhC-CCEECCcEEEE
Confidence            3578899999999999999999999999999999999885 678999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.+...
T Consensus        87 ~~a~~~~~   94 (102)
T 2cqb_A           87 NLAKPMRI   94 (102)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99997653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.65  E-value=4.5e-16  Score=133.78  Aligned_cols=84  Identities=20%  Similarity=0.285  Sum_probs=78.0

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeE--------EEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCC
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS  751 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~--------v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~  751 (787)
                      .+..+.++|||+|||..+|+++|+++|++||.|..        ++|+.+. .+|+++|||||+|.+.++|.+|++.|| +
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-~~g~~~G~afV~f~~~~~a~~Ai~~l~-g   85 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR-ETGKLKGEATVSFDDPPSAKAAIDWFD-G   85 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECT-TTCSEEEEEEEEBSSHHHHHHHHHHHT-T
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecC-CCCCeeeEEEEEECCHHHHHHHHHHhC-C
Confidence            34567899999999999999999999999999999        9999885 689999999999999999999999997 7


Q ss_pred             eeecCceEEEEEcc
Q psy3345         752 THLYGRRLVLEWAE  765 (787)
Q Consensus       752 ~~~~Gr~l~v~~A~  765 (787)
                      ..+.|++|+|+||+
T Consensus        86 ~~~~g~~l~V~~A~   99 (99)
T 2la6_A           86 KEFSGNPIKVSFAT   99 (99)
T ss_dssp             CBSSSSBCEEEECC
T ss_pred             CEeCCcEEEEEecC
Confidence            99999999999985

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.6e-16  Score=133.00  Aligned_cols=81  Identities=17%  Similarity=0.324  Sum_probs=73.3

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhc-CCeeecCceE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC-QSTHLYGRRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~-~~~~~~Gr~l  759 (787)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|+++       ||||||+|.+.++|..|+..|+ ++..+.|++|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            3457899999999999999999999999999999998775       7999999999999999999875 3678999999


Q ss_pred             EEEEccccc
Q psy3345         760 VLEWAEEAD  768 (787)
Q Consensus       760 ~v~~A~~~~  768 (787)
                      .|+||.++.
T Consensus        84 ~V~~a~~~~   92 (101)
T 2cq1_A           84 YIQYSNHKE   92 (101)
T ss_dssp             EEEECSCSS
T ss_pred             EEEEcCccc
Confidence            999998654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.3e-16  Score=134.82  Aligned_cols=86  Identities=27%  Similarity=0.511  Sum_probs=79.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|..|+|+++. .++.++|||||+|.++++|.+|+..|| +..+.|++|+|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v   86 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-ETQRSRGFGFVTFENIDDAKDAMMAMN-GKSVDGRQIRV   86 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS-SSCSCCSEEEEECSSHHHHHHHHHHHT-TCCTTSCCCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-CCCCcccEEEEEECCHHHHHHHHHHhC-CCEECCeEEEE
Confidence            4567999999999999999999999999999999999985 678999999999999999999999997 69999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.+...
T Consensus        87 ~~a~~~~~   94 (102)
T 1x5s_A           87 DQAGKSSD   94 (102)
T ss_dssp             EEEECCCC
T ss_pred             EECCCCCC
Confidence            99987654

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.65  E-value=7.7e-16  Score=133.97  Aligned_cols=81  Identities=15%  Similarity=0.225  Sum_probs=77.6

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC---c
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS---S   86 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~---~   86 (787)
                      .++..|+|.|     ||+++|+++|+++|+.||.|..|.|+.+++|+++|||||.|.+.++|.+||+.||+..+.|   +
T Consensus        13 ~~~~~l~v~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~   87 (105)
T 2dnh_A           13 GRDRKLFVGM-----LNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASS   87 (105)
T ss_dssp             CCCCEEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSS
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCc
Confidence            4577899999     9999999999999999999999999999999999999999999999999999999999998   9


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|.+
T Consensus        88 ~l~V~~a~~   96 (105)
T 2dnh_A           88 SLVVKFADT   96 (105)
T ss_dssp             CCEEEESCS
T ss_pred             cEEEEECcc
Confidence            999999987

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.7e-16  Score=134.39  Aligned_cols=85  Identities=20%  Similarity=0.403  Sum_probs=79.1

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEE-EeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFV-RLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v-~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      .+.++|||.|||..+|+++|+++|+.||.|.++ +|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v   80 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP-DTGNSKGYAFINFASFDASDAAIEAMN-GQYLCNRPITV   80 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT-TTCSCCSEEEEEBSSHHHHHHHHHTTT-TCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcC-CCCCcCeEEEEEECCHHHHHHHHHHcC-CCEECCEEEEE
Confidence            367899999999999999999999999999999 999885 689999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus        81 ~~a~~~~~   88 (96)
T 1x5t_A           81 SYAFKKDS   88 (96)
T ss_dssp             EESCCCCC
T ss_pred             EEecccCC
Confidence            99987664

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6.8e-17  Score=143.33  Aligned_cols=79  Identities=16%  Similarity=0.205  Sum_probs=74.0

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCce----EEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTV----TDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i----~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      +..+|+|+|     |||++|++||++||+.||.|    .+|+|+++++|+++|||||.|.+.++|++||+. |+..|+||
T Consensus        22 ~~~~v~V~n-----Lp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR   95 (123)
T 2dha_A           22 NQVIVRMRG-----LPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKR   95 (123)
T ss_dssp             SCCEEEECS-----CCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSC
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCe
Confidence            456799999     99999999999999999875    699999999999999999999999999999998 99999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      +|+|..|.+
T Consensus        96 ~i~V~~a~~  104 (123)
T 2dha_A           96 YIELFRSTA  104 (123)
T ss_dssp             EECCEEECH
T ss_pred             EEEEEECCH
Confidence            999999875

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.65  E-value=9.3e-17  Score=135.33  Aligned_cols=81  Identities=16%  Similarity=0.340  Sum_probs=71.4

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcC--CeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G--~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      .+|||+|||..+|+++|+++|+.||  .|.+++|+.+. .+|+++|||||+|.+.++|.+|++.|| +..+.|+.|.|.+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~-~~g~~kG~afV~f~~~~~a~~Ai~~l~-g~~~~gr~i~V~~   79 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR-ANGQSKGFALVGVGSEASSKKLMDLLP-KRELHGQNPVVTP   79 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECT-TTCCEEEEEEECC-CHHHHHHHHHHGG-GSCSSSCCCEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecC-CCCccCcEEEEEECCHHHHHHHHHHcC-CCeeCCEEEEEEE
Confidence            4799999999999999999999999  99999999985 689999999999999999999999997 7999999999999


Q ss_pred             ccccc
Q psy3345         764 AEEAD  768 (787)
Q Consensus       764 A~~~~  768 (787)
                      |.+..
T Consensus        80 ~~~~~   84 (90)
T 3p5t_L           80 SNKLE   84 (90)
T ss_dssp             C----
T ss_pred             CCCCc
Confidence            98764

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=6.7e-16  Score=133.83  Aligned_cols=82  Identities=20%  Similarity=0.272  Sum_probs=78.1

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..++..|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus        12 ~~~~~~l~V~n-----lp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   86 (103)
T 2cq0_A           12 ADDNATIRVTN-----LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI   86 (103)
T ss_dssp             CSSSEEEEEES-----CCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            34677899999     99999999999999999999999999987 7999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.++++
T Consensus        87 l~v~~a~~   94 (103)
T 2cq0_A           87 LNVEWAKP   94 (103)
T ss_dssp             CEEEESSC
T ss_pred             EEEEECCC
Confidence            99999987

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.4e-16  Score=135.80  Aligned_cols=86  Identities=24%  Similarity=0.473  Sum_probs=79.3

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...++++|||+|||..+|+++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   96 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAAMEGLN-GQDLMGQPIS   96 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTSSEEEEEEEEESCHHHHHHHHHHHT-TCBSSSSBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecC-CCCceeeEEEEEECCHHHHHHHHHHhc-CCEECCcEEE
Confidence            34567899999999999999999999999999999999885 679999999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.++.
T Consensus        97 V~~a~~~~  104 (106)
T 1p27_B           97 VDWCFVRG  104 (106)
T ss_dssp             EEESEESS
T ss_pred             EEeecCCC
Confidence            99998654

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.65  E-value=4.5e-16  Score=137.86  Aligned_cols=86  Identities=16%  Similarity=0.371  Sum_probs=79.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|+|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~V   99 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK-QTNLSKCFGFVSYDNPVSAQAAIQSMN-GFQIGMKRLKV   99 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECS-SSCSEEEEEEEECSSHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCCcCccEEEEECCHHHHHHHHHHcC-CCEECCEEEEE
Confidence            3467899999999999999999999999999999999885 589999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpz_A          100 QLKRSKND  107 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EEcCCCCc
Confidence            99997764

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.65  E-value=6e-16  Score=136.89  Aligned_cols=81  Identities=25%  Similarity=0.335  Sum_probs=77.7

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .++..|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+++|+++|||||.|.+.++|++|++.||+..|.|+.|.
T Consensus         5 ~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~   79 (116)
T 2fy1_A            5 DHPGKLFIGG-----LNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIK   79 (116)
T ss_dssp             CSCCEEEEEC-----CTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCE
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3467899999     99999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|++
T Consensus        80 V~~a~~   85 (116)
T 2fy1_A           80 VEQAKK   85 (116)
T ss_dssp             EEECCC
T ss_pred             EEECCC
Confidence            999987

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.65  E-value=5.8e-16  Score=135.99  Aligned_cols=86  Identities=26%  Similarity=0.481  Sum_probs=79.7

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||+|||..+|+++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~   99 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAAKEALN-GAEIMGQTIQ   99 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCT-TTSSBCSEEEEEESSHHHHHHHHHHHT-TCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCCcceEEEEEECCHHHHHHHHHHcC-CCEECCcEEE
Confidence            34567899999999999999999999999999999998885 689999999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.++.
T Consensus       100 V~~a~~~~  107 (110)
T 1oo0_B          100 VDWCFVKG  107 (110)
T ss_dssp             EEESEESS
T ss_pred             EEEcccCC
Confidence            99998654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4e-16  Score=135.23  Aligned_cols=86  Identities=27%  Similarity=0.532  Sum_probs=79.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v   89 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK-TTGQSKGFAFISFHRREDAARAIAGVS-GFGYDHLILNV   89 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHHHHHTT-TCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecC-CCCceeeEEEEEECCHHHHHHHHHHcC-CCeeCCcEEEE
Confidence            4567999999999999999999999999999999999885 589999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus        90 ~~a~~~~~   97 (103)
T 2cq0_A           90 EWAKPSTN   97 (103)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99997653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.65  E-value=7e-16  Score=136.67  Aligned_cols=87  Identities=24%  Similarity=0.508  Sum_probs=80.4

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   88 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDM-ATGKSKGYGFVSFFNKWDAENAIQQMG-GQWLGGRQIR   88 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHTT-TCEETTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCCcceEEEEEECCHHHHHHHHHHhC-CCEECCEEEE
Confidence            34578999999999999999999999999999999999885 589999999999999999999999997 6999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |.||.++..
T Consensus        89 V~~a~~~~~   97 (115)
T 2dgo_A           89 TNWATRKPP   97 (115)
T ss_dssp             EEESSCCCC
T ss_pred             EEEccCCCC
Confidence            999987654

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.65  E-value=6.2e-16  Score=134.57  Aligned_cols=85  Identities=25%  Similarity=0.414  Sum_probs=78.7

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC---ce
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG---RR  758 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G---r~  758 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+..|| +..+.|   ++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~gg~~~~   88 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP--DGSSKGCAFVKFSSHTEAQAAIHALH-GSQTMPGASSS   88 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS--SSCEEEEEEEEESSHHHHHHHHHHHS-SCCCCTTCSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC--CCCcCcEEEEEeCCHHHHHHHHHHHc-CCccCCCCCcc
Confidence            3568999999999999999999999999999999999984  79999999999999999999999997 688888   99


Q ss_pred             EEEEEcccccc
Q psy3345         759 LVLEWAEEADN  769 (787)
Q Consensus       759 l~v~~A~~~~~  769 (787)
                      |.|.||.++..
T Consensus        89 l~V~~a~~~~~   99 (105)
T 2dnh_A           89 LVVKFADTDKE   99 (105)
T ss_dssp             CEEEESCSSCC
T ss_pred             EEEEECccCcc
Confidence            99999997654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=5.9e-16  Score=132.83  Aligned_cols=81  Identities=21%  Similarity=0.361  Sum_probs=76.6

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCC--C--CcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE--G--KFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~--g--~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .++..|+|.|     ||+++|+++|+++|+.||.|..|.|+.+++  |  +++|||||.|.+.++|.+|++.||+..|+|
T Consensus         3 ~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (98)
T 2cpf_A            3 SGSSGLFIKN-----LNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG   77 (98)
T ss_dssp             CCCCCEEEES-----CCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            4678899999     999999999999999999999999999774  5  899999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus        78 ~~l~V~~a~~   87 (98)
T 2cpf_A           78 HKLEVRISER   87 (98)
T ss_dssp             EECEEECSSC
T ss_pred             eEEEEEEccC
Confidence            9999999987

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.8e-16  Score=135.00  Aligned_cols=82  Identities=20%  Similarity=0.296  Sum_probs=72.0

Q ss_pred             CCCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc--C
Q psy3345           4 HLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN--T   81 (787)
Q Consensus         4 ~~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~--~   81 (787)
                      |--|...++.+|+|.|     ||+++||+||+++|+.||.|++|.|+.+     +|||||.|.+.++|.+|++.|++  .
T Consensus         8 ~~~~~~~~~~~LfV~n-----Lp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~   77 (105)
T 1sjq_A            8 HHHGSGVPSRVIHIRK-----LPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTP   77 (105)
T ss_dssp             ----CCCCCCEEEECS-----CCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCC
T ss_pred             cccCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCc
Confidence            3334455688899999     9999999999999999999999999875     79999999999999999998864  7


Q ss_pred             ccCCceEEEEEccC
Q psy3345          82 YVFSSRIKVEKCSN   95 (787)
Q Consensus        82 ~~~~~~i~v~~~~~   95 (787)
                      .|.||.|.|.+|++
T Consensus        78 ~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           78 VLRGQPIYIQFSNH   91 (105)
T ss_dssp             EETTEECCBCCCSS
T ss_pred             eECCEEEEEEEcCC
Confidence            89999999999986

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.65  E-value=4.9e-16  Score=131.66  Aligned_cols=83  Identities=24%  Similarity=0.464  Sum_probs=77.6

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|++||.|.+++|+++   +|.++|||||+|.+.++|.+|+..|+ +..+.|++|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~---~g~~~g~afV~f~~~~~a~~a~~~l~-g~~~~g~~l~v   80 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVAERACRMMN-GMKLSGREIDV   80 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES---SSCEEEEEEEEESSHHHHHHHHHHHT-TCCBTTBCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc---CCCcceEEEEEECCHHHHHHHHHHhC-CCEECCcEEEE
Confidence            457899999999999999999999999999999999875   78999999999999999999999997 69999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      +||++..
T Consensus        81 ~~a~~~~   87 (92)
T 2dgv_A           81 RIDRNAS   87 (92)
T ss_dssp             EECSCCS
T ss_pred             EEcCCCC
Confidence            9998765

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=7.1e-16  Score=133.96  Aligned_cols=84  Identities=12%  Similarity=0.139  Sum_probs=79.4

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhc-cCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCc-cCC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEE-KGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY-VFS   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~-~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~-~~~   85 (787)
                      +..++.+|+|.|     ||+++|+++|+++|+. ||.|.+|+|+.+++|+++|||||.|.+.++|.+|++.||+.. |.|
T Consensus         5 ~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g   79 (104)
T 2dhg_A            5 SSGPEYSLFVGD-----LTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGS   79 (104)
T ss_dssp             CSSCCCCEEEEC-----CCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS
T ss_pred             CCCCCcEEEEeC-----CCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCC
Confidence            345678899999     9999999999999999 999999999999999999999999999999999999999999 999


Q ss_pred             ceEEEEEccCC
Q psy3345          86 SRIKVEKCSNL   96 (787)
Q Consensus        86 ~~i~v~~~~~~   96 (787)
                      +.|.|.++.+.
T Consensus        80 ~~l~v~~a~~~   90 (104)
T 2dhg_A           80 KPVRLSVAIPK   90 (104)
T ss_dssp             SCCCCCBCCCC
T ss_pred             EeEEEEEccCC
Confidence            99999999873

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=6e-16  Score=134.12  Aligned_cols=82  Identities=22%  Similarity=0.328  Sum_probs=77.7

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..+...|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|.|+.
T Consensus        10 ~~~~~~l~V~n-----Lp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   84 (103)
T 2dnm_A           10 VDGMITLKVDN-----LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRE   84 (103)
T ss_dssp             CSCCCEEEEES-----CCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBC
T ss_pred             CCCCeEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            34567899999     99999999999999999999999999987 5999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|++
T Consensus        85 l~V~~a~~   92 (103)
T 2dnm_A           85 LRVQVARY   92 (103)
T ss_dssp             CEEEECSS
T ss_pred             EEEEECCc
Confidence            99999987

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=8e-16  Score=135.40  Aligned_cols=83  Identities=14%  Similarity=0.205  Sum_probs=78.1

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhc------cC
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFN------NT   81 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~------~~   81 (787)
                      ..++..|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+||+.||      +.
T Consensus        12 ~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~   86 (111)
T 1x4h_A           12 VTEGKTVFIRN-----LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   86 (111)
T ss_dssp             CCCCCCEEEES-----CCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCCEEEEEC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCc
Confidence            34677899999     99999999999999999999999999987 68999999999999999999999999      99


Q ss_pred             ccCCceEEEEEccCC
Q psy3345          82 YVFSSRIKVEKCSNL   96 (787)
Q Consensus        82 ~~~~~~i~v~~~~~~   96 (787)
                      .|+|+.|.|.+|.+.
T Consensus        87 ~~~g~~l~v~~a~~~  101 (111)
T 1x4h_A           87 KLDGRQLKVDLAVTR  101 (111)
T ss_dssp             ESSSCEEEEECCCCC
T ss_pred             EEcCEEEEEEECCCC
Confidence            999999999999873

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.3e-15  Score=132.08  Aligned_cols=85  Identities=19%  Similarity=0.370  Sum_probs=77.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+++.   +.++|||||+|.+.++|.+|+..|+ +..+.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   86 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH---TSNDPYCFVEFYEHRDAAAALAAMN-GRKILGKEVK   86 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC---CSSCCEEEEEESSHHHHHHHHHHHT-TEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC---CCCCCEEEEEECCHHHHHHHHHHhC-CCCcCCCeEE
Confidence            34578999999999999999999999999999999999983   4479999999999999999999997 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.+...
T Consensus        87 V~~a~~~~~   95 (103)
T 2cqi_A           87 VNWATTPSS   95 (103)
T ss_dssp             EEECCCTTC
T ss_pred             EEECCCCcc
Confidence            999987553

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.64  E-value=6.3e-16  Score=135.08  Aligned_cols=83  Identities=14%  Similarity=0.283  Sum_probs=78.3

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .+..+...|+|.|     ||+.+|+++|+++|+.||.|..|+|+.+++|+++|||||.|.+.++|.+|++.||+..|+|+
T Consensus        24 ~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   98 (107)
T 3ulh_A           24 AGVETGGKLLVSN-----LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR   98 (107)
T ss_dssp             CCCCCSEEEEEES-----CCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            3445677899999     99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEcc
Q psy3345          87 RIKVEKCS   94 (787)
Q Consensus        87 ~i~v~~~~   94 (787)
                      .|.|.+|.
T Consensus        99 ~l~V~~a~  106 (107)
T 3ulh_A           99 PMNIQLVT  106 (107)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEeC
Confidence            99999985

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.6e-16  Score=133.69  Aligned_cols=81  Identities=20%  Similarity=0.308  Sum_probs=77.3

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEE-EEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDV-QLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~-~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      .++.+|+|.|     ||+++|+++|+++|+.||.|.+| +|+.++ +|+++|||||.|.+.++|.+|++.||+..|.|+.
T Consensus         3 ~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   77 (96)
T 1x5t_A            3 SGSSGIFIGN-----LDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRP   77 (96)
T ss_dssp             SCCCEEEEEC-----CCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEE
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3578899999     99999999999999999999999 999985 8999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus        78 l~v~~a~~   85 (96)
T 1x5t_A           78 ITVSYAFK   85 (96)
T ss_dssp             CEEEESCC
T ss_pred             EEEEEecc
Confidence            99999987

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.4e-15  Score=131.81  Aligned_cols=84  Identities=18%  Similarity=0.392  Sum_probs=78.1

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      +.+..+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++.+ ++|||||.|.+.++|.+|++.||+..|+|
T Consensus         9 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cq3_A            9 SESKSTPKRLHVSN-----IPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEG   82 (103)
T ss_dssp             SCCSCCCCEEEEES-----CCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34455678899999     9999999999999999999999999998755 99999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|.+
T Consensus        83 ~~l~v~~a~~   92 (103)
T 2cq3_A           83 RKIEVNNATA   92 (103)
T ss_dssp             EECEEEECCS
T ss_pred             EEEEEEEccc
Confidence            9999999987

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=4.7e-16  Score=134.78  Aligned_cols=85  Identities=24%  Similarity=0.413  Sum_probs=79.0

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|..|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~V   87 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP-HTKAPRGFAFVRFHDRRDAQDAEAAMD-GAELDGRELRV   87 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCS-SSCSBCSCEEEEESSSSHHHHHHHHHS-SCCBTTBCCEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-CCCCCCeEEEEEECCHHHHHHHHHHcC-CCEECCcEEEE
Confidence            4567999999999999999999999999999999999885 579999999999999999999999997 69999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      +||.+..
T Consensus        88 ~~a~~~~   94 (103)
T 2dnm_A           88 QVARYGR   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EECCcCC
Confidence            9998654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.64  E-value=6.2e-16  Score=134.85  Aligned_cols=87  Identities=21%  Similarity=0.418  Sum_probs=79.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee---cCc
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL---YGR  757 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~---~Gr  757 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+   .|+
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~~~~~g~   86 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDR-FTGMHKGCAFLTYCERESALKAQSALH-EQKTLPGMNR   86 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCS-SSCSCCSEEEEEESSHHHHHHHHHHHT-TTCCCTTCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-CCCCcceEEEEEECCHHHHHHHHHHhc-CCcccCCCCc
Confidence            34577999999999999999999999999999999999986 579999999999999999999999997 5776   889


Q ss_pred             eEEEEEcccccc
Q psy3345         758 RLVLEWAEEADN  769 (787)
Q Consensus       758 ~l~v~~A~~~~~  769 (787)
                      +|.|.||.++..
T Consensus        87 ~l~v~~a~~~~~   98 (106)
T 2dgp_A           87 PIQVKPADSESR   98 (106)
T ss_dssp             CCEEEECCCCSC
T ss_pred             eEEEEECCcccc
Confidence            999999987654

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=9.7e-16  Score=134.87  Aligned_cols=88  Identities=26%  Similarity=0.548  Sum_probs=80.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-----Ceeec
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-----STHLY  755 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-----~~~~~  755 (787)
                      ...+.++|||+|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..||.     +..+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP-DTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            34578899999999999999999999999999999999886 6789999999999999999999999951     59999


Q ss_pred             CceEEEEEcccccc
Q psy3345         756 GRRLVLEWAEEADN  769 (787)
Q Consensus       756 Gr~l~v~~A~~~~~  769 (787)
                      |++|.|.||.++..
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            99999999997764

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.6e-16  Score=136.19  Aligned_cols=81  Identities=20%  Similarity=0.350  Sum_probs=73.7

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-CeeecCceE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-STHLYGRRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-~~~~~Gr~l  759 (787)
                      ...++++|||+|||+.+|+++|+++|++||.|.+|+|+++       ||||||+|.+.++|.+|+..|++ +..+.|++|
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-------CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            3457899999999999999999999999999999999876       79999999999999999999863 368999999


Q ss_pred             EEEEccccc
Q psy3345         760 VLEWAEEAD  768 (787)
Q Consensus       760 ~v~~A~~~~  768 (787)
                      .|+||++++
T Consensus       100 ~V~~a~~k~  108 (119)
T 2ad9_A          100 YIQFSNHKE  108 (119)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEccCCC
Confidence            999998665

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=6.2e-16  Score=134.26  Aligned_cols=87  Identities=23%  Similarity=0.499  Sum_probs=78.7

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      .+..+.++|||.|||..+|+++|+++|+.|| |.+|+|+.+...+|+++|||||+|.+.++|.+|| .|| +..+.|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~-g~~~~g~~l   86 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-EESLGNKRI   86 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGG-TCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcC-CCEeCCcEE
Confidence            3445779999999999999999999999999 9999999986223999999999999999999999 897 699999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||.++..
T Consensus        87 ~V~~a~~~~~   96 (104)
T 1wi8_A           87 RVDVADQAQD   96 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            9999997764

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.4e-16  Score=135.32  Aligned_cols=90  Identities=27%  Similarity=0.518  Sum_probs=82.3

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      +.++|||+|||..+|+++|+++|+.||.|.+++|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|+.|.|+|
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v~~   84 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQETALSAMRNLN-GREFSGRALRVDN   84 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET-TTTEEEEEEEEECSCHHHHHHHHHHSS-SBSCSSSCBEEEE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCC-CCCccceEEEEEECCHHHHHHHHHHhC-CCeeCCcEEEEEe
Confidence            45789999999999999999999999999999999885 589999999999999999999999997 7999999999999


Q ss_pred             ccccccHHHHHH
Q psy3345         764 AEEADNVEDIRK  775 (787)
Q Consensus       764 A~~~~~~~~~~~  775 (787)
                      |.+.......+.
T Consensus        85 a~~~~~~~~~~~   96 (104)
T 1p1t_A           85 AASEKNKEELKS   96 (104)
T ss_dssp             TTCTTHHHHHHH
T ss_pred             CCCccchhhhcc
Confidence            998887655543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=6.2e-16  Score=132.72  Aligned_cols=86  Identities=27%  Similarity=0.481  Sum_probs=78.1

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCC--CCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG--SGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~--~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      .+.++|||+|||..+|+++|+++|+.||.|.+|+|+.+...  ++.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQ-GHTVDGHKLE   81 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHST-TCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhC-CCeeCCeEEE
Confidence            46789999999999999999999999999999999988632  44899999999999999999999997 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.+...
T Consensus        82 V~~a~~~~~   90 (98)
T 2cpf_A           82 VRISERATK   90 (98)
T ss_dssp             EECSSCSSC
T ss_pred             EEEccCCCC
Confidence            999987653

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.64  E-value=5.4e-16  Score=130.20  Aligned_cols=84  Identities=19%  Similarity=0.435  Sum_probs=75.9

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||..+|+++|+++|++||.|.+++|+.+....++++|||||+|.+.++|.+|+..|| +..+.|+.|.|+|
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v~~   81 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMD-GGQIDGQEITATA   81 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHT-TCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcC-CCeECCeEEEEEE
Confidence            468999999999999999999999999999999998852223489999999999999999999997 7999999999999


Q ss_pred             ccccc
Q psy3345         764 AEEAD  768 (787)
Q Consensus       764 A~~~~  768 (787)
                      |.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            98654

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.64  E-value=4.5e-16  Score=130.67  Aligned_cols=81  Identities=11%  Similarity=0.249  Sum_probs=75.7

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCC-C-CcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-G-KFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~-g-~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +.+.+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++. + +++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus         2 ~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   76 (88)
T 4a8x_A            2 MKPTKVHIGR-----LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQE   76 (88)
T ss_dssp             CCCCEEEEEC-----CCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeE
Confidence            4567899999     999999999999999999999999999873 3 49999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.++.+
T Consensus        77 l~v~~a~~   84 (88)
T 4a8x_A           77 ITATAVLA   84 (88)
T ss_dssp             CEEEEECC
T ss_pred             EEEEECCC
Confidence            99999986

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=1.3e-15  Score=131.95  Aligned_cols=83  Identities=17%  Similarity=0.358  Sum_probs=77.5

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      ..|..+...|+|.|     ||+++|+++|+++|+.|| |.+|+|+.++ +|+++|||||.|.+.++|.+|| .||+..|+
T Consensus         9 ~~~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~   81 (103)
T 2dng_A            9 ELPTEPPYTAYVGN-----LPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLG   81 (103)
T ss_dssp             CCCSSSCEEEEEES-----CCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCCCCCeEEEEeC-----CCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeEC
Confidence            34556778899999     999999999999999997 9999999988 6999999999999999999999 89999999


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      |+.|.|.+|.+
T Consensus        82 g~~l~V~~a~~   92 (103)
T 2dng_A           82 DRSLRVDIAEG   92 (103)
T ss_dssp             TEECEEEECCC
T ss_pred             CeEEEEEEecC
Confidence            99999999987

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.2e-15  Score=130.20  Aligned_cols=83  Identities=20%  Similarity=0.315  Sum_probs=75.6

Q ss_pred             CCCCCEEEEecCCccCcHHHHH----HHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVE----ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~----~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      ....++|||+|||..+|+++|+    ++|++||.|.+|+|+.+.  .+  +|||||+|.+.++|.+|+..|| +..+.|+
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~--~~--rg~afV~f~~~~~A~~Ai~~l~-g~~~~gr   80 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT--DY--QLKAVVQMENLQDAIGAVNSLH-RYKIGSK   80 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCC--ST--TCCEEEEESSHHHHHHHHHHHT-TEEETTE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCC--CC--CeEEEEEECCHHHHHHHHHHhC-CCEECCe
Confidence            4467899999999999999999    999999999999999884  23  8999999999999999999997 7999999


Q ss_pred             eEEEEEcccccc
Q psy3345         758 RLVLEWAEEADN  769 (787)
Q Consensus       758 ~l~v~~A~~~~~  769 (787)
                      +|+|+||++...
T Consensus        81 ~l~V~~a~~~~~   92 (96)
T 2dgx_A           81 KILVSLATGASG   92 (96)
T ss_dssp             EEEEEECCCSSC
T ss_pred             EEEEEEcCCCCC
Confidence            999999987643

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=6.3e-16  Score=134.00  Aligned_cols=85  Identities=20%  Similarity=0.392  Sum_probs=79.0

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+   +|.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~   86 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME---GGRSKGFGFVCFSSPEEATKAVTEMN-GRIVATKPLY   86 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC---SSSEEEEEEEEESSHHHHHHHHHHHT-TCBSSSSBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---CCCcCEEEEEEECCHHHHHHHHHHhC-CCEeCCcEEE
Confidence            3457899999999999999999999999999999999887   78899999999999999999999997 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.++..
T Consensus        87 V~~a~~~~~   95 (103)
T 2d9p_A           87 VALAQRKEE   95 (103)
T ss_dssp             EEECSSCCC
T ss_pred             EEEeccccc
Confidence            999997664

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.64  E-value=3.9e-16  Score=131.35  Aligned_cols=80  Identities=23%  Similarity=0.354  Sum_probs=75.9

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      ..+..|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|+ .||+..|+|+.|
T Consensus         4 ~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l   77 (89)
T 3ucg_A            4 ADARSIYVGN-----VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQI   77 (89)
T ss_dssp             HHHTEEEEES-----CCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEEC
T ss_pred             CcCCEEEEeC-----CCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEE
Confidence            3467899999     99999999999999999999999999987 8999999999999999999999 899999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.++++
T Consensus        78 ~V~~a~~   84 (89)
T 3ucg_A           78 KVIPKRT   84 (89)
T ss_dssp             EEEETTT
T ss_pred             EEEEccC
Confidence            9999986

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=1.3e-15  Score=133.12  Aligned_cols=83  Identities=19%  Similarity=0.392  Sum_probs=78.2

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEec-C-CCCcceEEEEEecCHHHHHHHHHHh-ccCccC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYT-T-EGKFRRFAFIGYHREDQAQAALDYF-NNTYVF   84 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~-~-~g~~~g~afv~f~~~~~a~~a~~~~-~~~~~~   84 (787)
                      +..+..+|+|.|     ||+.+|+++|+++|+.||.|..|+|+.+ + +|+++|||||.|.+.++|.+|+..| |+..|.
T Consensus        11 ~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~   85 (107)
T 2cph_A           11 KKQTTSKILVRN-----IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY   85 (107)
T ss_dssp             CSSCCCCEEEES-----CCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS
T ss_pred             cCCCCCEEEEeC-----CCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeEC
Confidence            445677899999     9999999999999999999999999998 4 8999999999999999999999999 999999


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      |+.|.|.+|++
T Consensus        86 g~~l~v~~a~~   96 (107)
T 2cph_A           86 GRRLVLEWADS   96 (107)
T ss_dssp             SCBCEEEECCC
T ss_pred             CCEEEEEeCCC
Confidence            99999999987

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.63  E-value=1.2e-15  Score=137.16  Aligned_cols=83  Identities=13%  Similarity=0.264  Sum_probs=79.1

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +..++.+|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.+++|+++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus        31 ~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  105 (124)
T 2kt5_A           31 GVETGAKLLVSN-----LDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRP  105 (124)
T ss_dssp             CCSSCEEEEEES-----CCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCE
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            445677899999     999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus       106 l~V~~a~~  113 (124)
T 2kt5_A          106 MDIQLVAS  113 (124)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEeCC
Confidence            99999987

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.6e-15  Score=131.35  Aligned_cols=86  Identities=29%  Similarity=0.462  Sum_probs=78.1

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ....+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+.   +.++|||||+|.+.++|.+|+..|| +..+.|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l   85 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE---RGSKGFGFVTFENSADADRAREKLH-GTVVEGRKI   85 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT---TTTCCEEEEEESCHHHHHHHHHHHT-TCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCcEEEEEEECCHHHHHHHHHHhC-CCEECCEEE
Confidence            345578999999999999999999999999999999999883   3489999999999999999999997 799999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||.++..
T Consensus        86 ~v~~a~~~~~   95 (103)
T 2cq3_A           86 EVNNATARVM   95 (103)
T ss_dssp             EEEECCSSCC
T ss_pred             EEEEcccCCC
Confidence            9999987653

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.63  E-value=7e-16  Score=135.46  Aligned_cols=82  Identities=20%  Similarity=0.347  Sum_probs=77.4

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..++..|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus        23 ~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   97 (110)
T 1oo0_B           23 SVEGWILFVTS-----IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT   97 (110)
T ss_dssp             BTTBEEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            34566799999     99999999999999999999999999987 7999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus        98 l~V~~a~~  105 (110)
T 1oo0_B           98 IQVDWCFV  105 (110)
T ss_dssp             CEEEESEE
T ss_pred             EEEEEccc
Confidence            99999987

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.63  E-value=7e-16  Score=131.57  Aligned_cols=82  Identities=26%  Similarity=0.399  Sum_probs=76.6

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|++||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~V   89 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR--EGKPKSFGFVCFKHPESVSYAIALLN-GIRLYGRPINV   89 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT--TSCEEEEEEEEESSTHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC--CCCCceEEEEEECCHHHHHHHHHHhC-CCEECCCEEEE
Confidence            4467899999999999999999999999999999999985  58999999999999999999999997 79999999999


Q ss_pred             EEccc
Q psy3345         762 EWAEE  766 (787)
Q Consensus       762 ~~A~~  766 (787)
                      +||+.
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99963

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=3.8e-16  Score=134.03  Aligned_cols=82  Identities=15%  Similarity=0.136  Sum_probs=76.2

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..+..+|+|.|     ||+.+|+++|+++|+.||.|.++.++.++ +|+++|||||.|.+.++|++|++.||+..|+||.
T Consensus        12 ~~~~~~l~v~n-----Lp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   86 (98)
T 2cqp_A           12 KPGPTIIKVQN-----MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK   86 (98)
T ss_dssp             CCSSEEEEEES-----CCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            34567799999     99999999999999999999988888876 7999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.++..
T Consensus        87 l~V~~a~~   94 (98)
T 2cqp_A           87 VKLVLGSG   94 (98)
T ss_dssp             CEEEESSC
T ss_pred             EEEEEcCC
Confidence            99999975

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.63  E-value=2.4e-16  Score=134.48  Aligned_cols=82  Identities=15%  Similarity=0.147  Sum_probs=74.2

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..+..+|+|.|     ||+.+|++||+++|+.||.|..+.++.++ +|+++|||||.|.++++|++|++.||+..|+||.
T Consensus        12 ~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~   86 (95)
T 2ek1_A           12 KPGPTVIKVQN-----MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK   86 (95)
T ss_dssp             ---CEEEEEEC-----CCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcE
Confidence            33567899999     99999999999999999999988888876 7899999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.++..
T Consensus        87 l~v~~a~s   94 (95)
T 2ek1_A           87 VKLSGPSS   94 (95)
T ss_dssp             CEEECCC-
T ss_pred             EEEEeccC
Confidence            99998863

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.63  E-value=1.2e-16  Score=139.30  Aligned_cols=85  Identities=21%  Similarity=0.209  Sum_probs=78.6

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCc---eEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccC
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGT---VTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT   81 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~   81 (787)
                      ++.+......|+|.|     ||+++|++||+++|+.||.   |.+|+|+++++|+++|||||.|.+.++|++||+ +|+.
T Consensus         4 ~~~~~~~~~~l~V~n-----Lp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~   77 (107)
T 2lmi_A            4 LEEEVDDVFLIRAQG-----LPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRM   77 (107)
T ss_dssp             CCCCCSSCCEEEEEC-----CCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             CcCCCCCccEEEEeC-----CCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcc
Confidence            344555677899999     9999999999999999998   899999999999999999999999999999999 8999


Q ss_pred             ccCCceEEEEEccC
Q psy3345          82 YVFSSRIKVEKCSN   95 (787)
Q Consensus        82 ~~~~~~i~v~~~~~   95 (787)
                      .|+||.|.|..|.+
T Consensus        78 ~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           78 YMGQRYVEVYEINN   91 (107)
T ss_dssp             CSSSSCCCCEECCH
T ss_pred             eeCCeEEEEEECCH
Confidence            99999999999875

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.63  E-value=1.1e-15  Score=128.03  Aligned_cols=81  Identities=20%  Similarity=0.295  Sum_probs=74.4

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ....+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++. ++..|+|
T Consensus         6 ~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g   79 (87)
T 3s7r_A            6 KNEEDAGKMFVGG-----LSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDG   79 (87)
T ss_dssp             -CCSCTTEEEEEC-----CCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETT
T ss_pred             CCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECC
Confidence            3445678899999     99999999999999999999999999987 699999999999999999999976 8889999


Q ss_pred             ceEEEEEc
Q psy3345          86 SRIKVEKC   93 (787)
Q Consensus        86 ~~i~v~~~   93 (787)
                      +.|.|..|
T Consensus        80 ~~i~v~~A   87 (87)
T 3s7r_A           80 RVIDPKKA   87 (87)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEEEeC
Confidence            99999875

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=4.2e-16  Score=134.20  Aligned_cols=80  Identities=14%  Similarity=0.299  Sum_probs=74.7

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||+.+|+++|+++|++||.|.+|+|+++.  .|+++|||||+|.+.++|.+|+. ++ +..+.|+.|.|.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~--~g~~rG~aFV~F~~~e~a~~Ai~-~~-~~~~~gr~l~V~   84 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL--HKAFKGSIFVVFDSIESAKKFVE-TP-GQKYKETDLLIL   84 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCC--TTSCCCEEEEEESSHHHHHHHHT-SS-CCCCTTTTCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECC--CCCCccEEEEEECCHHHHHHHHH-cC-CCEECCEEEEEE
Confidence            356789999999999999999999999999999999995  49999999999999999999999 75 799999999999


Q ss_pred             Eccc
Q psy3345         763 WAEE  766 (787)
Q Consensus       763 ~A~~  766 (787)
                      |+.+
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            9975

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=6.5e-16  Score=132.87  Aligned_cols=86  Identities=17%  Similarity=0.329  Sum_probs=79.3

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCee-EEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce-
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR-  758 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~-~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~-  758 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|. +++|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|+. 
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~~   82 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNR-LTGIPAGYCFVEFADLATAEKCLHKIN-GKPLPGATP   82 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECS-SSCCEEEEEEEECSCHHHHHHHHHTTT-TSEESSCSS
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecC-CCCCcCCEEEEEeCCHHHHHHHHHHHc-CCccCCCCc
Confidence            345689999999999999999999999999999 99999885 689999999999999999999999997 79999999 


Q ss_pred             ---EEEEEccccc
Q psy3345         759 ---LVLEWAEEAD  768 (787)
Q Consensus       759 ---l~v~~A~~~~  768 (787)
                         |+|+||.+..
T Consensus        83 ~~~l~v~~a~~~~   95 (99)
T 2div_A           83 AKRFKLNYATYSG   95 (99)
T ss_dssp             CEECCEEETTCCS
T ss_pred             ceeEEEeecCCCC
Confidence               9999998653

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.63  E-value=6.1e-16  Score=139.40  Aligned_cols=83  Identities=23%  Similarity=0.364  Sum_probs=78.0

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      +..++..|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|++||+.||+..|+|+
T Consensus        42 ~~~~~~~l~V~n-----Lp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~  116 (129)
T 2kxn_B           42 NPDPNCCLGVFG-----LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR  116 (129)
T ss_dssp             CCCCSSCBCEET-----CTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            345677899999     99999999999999999999999999987 689999999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|.+
T Consensus       117 ~l~V~~a~~  125 (129)
T 2kxn_B          117 RIRVDFSIT  125 (129)
T ss_dssp             CCEESCCSS
T ss_pred             EEEEEEecC
Confidence            999999986

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=3e-16  Score=138.53  Aligned_cols=82  Identities=12%  Similarity=0.094  Sum_probs=77.5

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCce-EEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTV-TDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i-~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ...+...|+|.|     ||+++|++||+++|+.||.| .+|+|+++++|+++|||||.|.+.++|.+||+. |+..|+||
T Consensus        11 ~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr   84 (114)
T 2cpy_A           11 VNSAKVCAHITN-----IPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGR   84 (114)
T ss_dssp             CCSCCCEEEEES-----CCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTE
T ss_pred             CCCCccEEEEeC-----cCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCe
Confidence            345677899999     99999999999999999999 899999999999999999999999999999998 99999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|.+
T Consensus        85 ~i~v~~a~~   93 (114)
T 2cpy_A           85 EAFVHVVTL   93 (114)
T ss_dssp             EEEEEEECH
T ss_pred             EEEEEECCH
Confidence            999999986

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.63  E-value=9.3e-16  Score=132.87  Aligned_cols=86  Identities=26%  Similarity=0.441  Sum_probs=78.5

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      .+..+.++|||.|||..+|+++|+++|+.|| |.+|+|+++. .+|+++|||||+|.+.++|.+|+ .|| +..+.|++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A~-~l~-g~~~~g~~l   85 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK-DTDKFKGFCYVEFDEVDSLKEAL-TYD-GALLGDRSL   85 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECS-SSCSEEEEEEEEESSHHHHHHHG-GGT-TCEETTEEC
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecC-CCCccceEEEEEECCHHHHHHHH-hhC-CCeECCeEE
Confidence            3445789999999999999999999999997 9999999985 67999999999999999999999 896 799999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||.++..
T Consensus        86 ~V~~a~~~~~   95 (103)
T 2dng_A           86 RVDIAEGRKQ   95 (103)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEecCCCC
Confidence            9999997654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.63  E-value=1e-15  Score=128.95  Aligned_cols=79  Identities=14%  Similarity=0.162  Sum_probs=71.9

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCc--cC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY--VF   84 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~--~~   84 (787)
                      .+..|+..|+|+|     ||+.+|+++|+++|+.||.|++|.|+.     +||||||.|.+.++|.+|++.||+..  |+
T Consensus        16 ~~~~ps~~l~V~N-----Lp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~   85 (100)
T 3r27_A           16 HKTPASPVVHIRG-----LIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQIYIA   85 (100)
T ss_dssp             -CCCCCSEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCEEET
T ss_pred             ccCCCCcEEEEeC-----CCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCCceeC
Confidence            3445788899999     999999999999999999999999985     37999999999999999999999874  89


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      ||.|.|.+|+.
T Consensus        86 Gr~i~V~~S~~   96 (100)
T 3r27_A           86 GHPAFVNYSTS   96 (100)
T ss_dssp             TEEEEEEECSC
T ss_pred             CcEEEEEeccc
Confidence            99999999986

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.63  E-value=7.2e-16  Score=137.72  Aligned_cols=85  Identities=18%  Similarity=0.298  Sum_probs=76.1

Q ss_pred             cCCCCCEEEEecCCccCcHHHHH----HHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVE----ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG  756 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~----~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G  756 (787)
                      ...+.++|||+|||+.+++++|+    ++|++||.|.+|.+++    +|+++|||||+|.+.++|..|+..|| |..+.|
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~----~~~~rG~aFV~F~~~~~A~~Ai~~ln-g~~l~g   99 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL----SDDNSGKAYIVFATQESAQAFVEAFQ-GYPFQG   99 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC----CCSSCCCEEEEESSHHHHHHHHHHST-TCCCTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc----CCCcCCEEEEEECCHHHHHHHHHHHC-CCEeCC
Confidence            34568899999999999999876    7999999999998854    57899999999999999999999997 799999


Q ss_pred             ceEEEEEccccccH
Q psy3345         757 RRLVLEWAEEADNV  770 (787)
Q Consensus       757 r~l~v~~A~~~~~~  770 (787)
                      ++|+|+||.++...
T Consensus       100 r~l~V~~a~~~~~~  113 (127)
T 2a3j_A          100 NPLVITFSETPQSQ  113 (127)
T ss_dssp             SCCEEEECCCCCHH
T ss_pred             CEEEEEEccCcchh
Confidence            99999999987654

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.3e-15  Score=132.23  Aligned_cols=83  Identities=22%  Similarity=0.352  Sum_probs=77.4

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCC--CCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE--GKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~--g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ..|..+...|+|.|     ||+++|+++|+++|+.|| |.+|.|+.++.  |+++|||||.|.+.++|++|| .||+..|
T Consensus         9 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~   81 (104)
T 1wi8_A            9 RLPKSPPYTAFLGN-----LPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL   81 (104)
T ss_dssp             CCCSSSCEEEEEES-----CCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEE
T ss_pred             CCCCCCCCEEEEeC-----CCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEe
Confidence            34555778899999     999999999999999999 99999999884  999999999999999999999 8999999


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +|+.|.|.+|.+
T Consensus        82 ~g~~l~V~~a~~   93 (104)
T 1wi8_A           82 GNKRIRVDVADQ   93 (104)
T ss_dssp             TTEECEEEECCC
T ss_pred             CCcEEEEEEccC
Confidence            999999999987

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.63  E-value=9.4e-16  Score=133.16  Aligned_cols=84  Identities=21%  Similarity=0.357  Sum_probs=76.7

Q ss_pred             CCCCCEEEEecCCccC------cHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec
Q psy3345         682 KQTGSKILVRNIPFQA------KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY  755 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~------t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~  755 (787)
                      ....++|||+|||..+      |+++|+++|++||.|.+|+|++   .+|+++|||||+|.+.++|.+|+..|| |..+.
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~---~~g~~~G~afV~f~~~~~A~~Ai~~l~-g~~~~   87 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE---EDGKTKGYIFLEYASPAHAVDAVKNAD-GYKLD   87 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC---BTTBSCCEEEEEECSSSHHHHHHHHCS-SEECS
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC---CCCCeeeEEEEEECCHHHHHHHHHHhC-CcccC
Confidence            3457899999999999      8899999999999999999984   489999999999999999999999997 79999


Q ss_pred             Cc-eEEEEEcccccc
Q psy3345         756 GR-RLVLEWAEEADN  769 (787)
Q Consensus       756 Gr-~l~v~~A~~~~~  769 (787)
                      |+ +|.|+||...+.
T Consensus        88 g~~~l~V~~a~~~~k  102 (105)
T 2nlw_A           88 KQHTFRVNLFTDFDK  102 (105)
T ss_dssp             TTCEEEEECSCCCCC
T ss_pred             CCceEEEEEcchHhh
Confidence            98 999999986553

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.6e-15  Score=134.18  Aligned_cols=82  Identities=20%  Similarity=0.304  Sum_probs=78.0

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      ..++.+|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.+++|+++|||||.|.+.++|.+|++.||+..|.|+.|
T Consensus        12 ~~~~~~l~V~n-----lp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (114)
T 2do0_A           12 GRLGSTVFVAN-----LDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM   86 (114)
T ss_dssp             CCCCSCEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEE
Confidence            34567899999     9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.++..
T Consensus        87 ~v~~a~~   93 (114)
T 2do0_A           87 HVKMDER   93 (114)
T ss_dssp             EEEECSC
T ss_pred             EEEEccc
Confidence            9999975

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.63  E-value=1.2e-15  Score=135.02  Aligned_cols=83  Identities=23%  Similarity=0.395  Sum_probs=78.2

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||..+|+++|+++|+.||.|.+|+|+.+.  +|+++|||||+|.+.++|.+|+..|| +..+.|+.|.|+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~F~~~~~A~~Ai~~l~-g~~~~g~~l~V~   81 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR--TSKSRGFAFITFENPADAKNAAKDMN-GKSLHGKAIKVE   81 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST--TTTCCCEEEEECSSHHHHHHHHHHCS-SCBCSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC--CCCcccEEEEEECCHHHHHHHHHHhC-CCEECCEEEEEE
Confidence            467899999999999999999999999999999999984  89999999999999999999999997 799999999999


Q ss_pred             Eccccc
Q psy3345         763 WAEEAD  768 (787)
Q Consensus       763 ~A~~~~  768 (787)
                      ||++..
T Consensus        82 ~a~~~~   87 (116)
T 2fy1_A           82 QAKKPS   87 (116)
T ss_dssp             ECCCSS
T ss_pred             ECCCCC
Confidence            998665

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.3e-15  Score=135.07  Aligned_cols=84  Identities=18%  Similarity=0.166  Sum_probs=77.7

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ....+..+|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|++||+.+|+ .|.|
T Consensus        12 ~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g   85 (116)
T 2cqd_A           12 QKDTTFTKIFVGG-----LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG   85 (116)
T ss_dssp             CCSCSSSEEEEEC-----CCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT
T ss_pred             cCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCC
Confidence            3445677899999     99999999999999999999999999987 699999999999999999999999998 8999


Q ss_pred             ceEEEEEccCC
Q psy3345          86 SRIKVEKCSNL   96 (787)
Q Consensus        86 ~~i~v~~~~~~   96 (787)
                      +.|.|.+|.+.
T Consensus        86 ~~l~V~~a~~~   96 (116)
T 2cqd_A           86 RKANVNLAYLG   96 (116)
T ss_dssp             EECEEEESTTT
T ss_pred             EEEEEEEcccC
Confidence            99999999863

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=5.2e-16  Score=134.28  Aligned_cols=82  Identities=21%  Similarity=0.354  Sum_probs=73.5

Q ss_pred             CCCCCEEEEecCCcc-CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhc-CCeeecCceE
Q psy3345         682 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC-QSTHLYGRRL  759 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~-~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~-~~~~~~Gr~l  759 (787)
                      ..++++|||+|||++ +|+++|+++|++||.|.+|+|++.       ||||||+|.+.++|..|+..|+ ++..+.||+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            457899999999998 999999999999999999999754       7999999999999999999986 2456999999


Q ss_pred             EEEEccccccH
Q psy3345         760 VLEWAEEADNV  770 (787)
Q Consensus       760 ~v~~A~~~~~~  770 (787)
                      +|+||.++...
T Consensus        95 ~V~~a~~~~~~  105 (112)
T 1x4f_A           95 KVDLSEKYKKL  105 (112)
T ss_dssp             EEEEECSCSSS
T ss_pred             EEEECcccccc
Confidence            99999876653

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=8.1e-16  Score=134.87  Aligned_cols=87  Identities=25%  Similarity=0.419  Sum_probs=78.6

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCC-eeEEEec-cccCCCCCCceEEEEEecCHHHHHHHHHHhcCC-eeecCceE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLP-KKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS-THLYGRRL  759 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~-I~~v~i~-~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~-~~~~Gr~l  759 (787)
                      .+.++|||.|||..+|+++|+++|+.||. |.+++++ .+. .+|.++|||||+|.+.++|..|+..|+++ ..+.|++|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA-DKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC-TTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCC-CCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            46789999999999999999999999998 9999998 553 67899999999999999999999999534 89999999


Q ss_pred             EEEEccccccH
Q psy3345         760 VLEWAEEADNV  770 (787)
Q Consensus       760 ~v~~A~~~~~~  770 (787)
                      .|+||.++...
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999977653

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.62  E-value=1e-15  Score=140.67  Aligned_cols=86  Identities=22%  Similarity=0.455  Sum_probs=80.1

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||+|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|+|
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v  116 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR-ETRQSRGYGFVKFQSGSSAQQAIAGLN-GFNILNKRLKV  116 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET-TTTEEEEEEEEEESSHHHHHHHHHHTT-TEECSSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCCcceEEEEEECCHHHHHHHHHHhC-CCEECCeEEEE
Confidence            4467999999999999999999999999999999999885 578999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus       117 ~~a~~~~~  124 (139)
T 1u6f_A          117 ALAASGHQ  124 (139)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99997764

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.5e-15  Score=130.17  Aligned_cols=81  Identities=14%  Similarity=0.212  Sum_probs=75.7

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      ..+...|+|.|     ||+.+|+++|+++|+.||.|..|+|+.++.+ ++|||||.|.+.++|.+|++.||+..|.|+.|
T Consensus        12 ~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   85 (103)
T 2cqi_A           12 DGQPRTLYVGN-----LSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEV   85 (103)
T ss_dssp             SCCCCEEEEES-----CCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEeC-----CCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeE
Confidence            34567899999     9999999999999999999999999998644 79999999999999999999999999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.+|++
T Consensus        86 ~V~~a~~   92 (103)
T 2cqi_A           86 KVNWATT   92 (103)
T ss_dssp             EEEECCC
T ss_pred             EEEECCC
Confidence            9999987

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.62  E-value=3.3e-16  Score=139.11  Aligned_cols=81  Identities=21%  Similarity=0.274  Sum_probs=74.2

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceE--EEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVT--DVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~--~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ++.+...|+|+|     |||++|++||+++|+.|+ |.  +|+|+++++|+++|||||.|.++++|++||+. ++..|+|
T Consensus        38 ~~~~~~~lfVgn-----Lp~~~te~dL~~~F~~~~-i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~g  110 (126)
T 2hgm_A           38 DSANDGFVRLRG-----LPFGCTKEEIVQFFSGLE-IVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGH  110 (126)
T ss_dssp             CSSSCCEEEEEC-----CCTTCCHHHHHHHTTTSC-EEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTT
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHhcCC-ceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECC
Confidence            334567899999     999999999999999995 66  99999999999999999999999999999997 8899999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      |.|+|..+.+
T Consensus       111 R~I~V~~a~~  120 (126)
T 2hgm_A          111 RYIEVFKSSQ  120 (126)
T ss_dssp             BCCCCEEECH
T ss_pred             EEEEEEECCH
Confidence            9999998875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.62  E-value=8.3e-16  Score=143.20  Aligned_cols=80  Identities=15%  Similarity=0.263  Sum_probs=75.4

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccC--ceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKG--TVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      .+.+|+|.|     ||+++|+++|+++|+.||  .|.+|+|+.++ +|+++|||||.|.+.++|.+||+.||+..|+||.
T Consensus        54 ~~~~lfVgn-----Lp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~  128 (156)
T 3n9u_C           54 RRAAVYVGS-----FSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK  128 (156)
T ss_dssp             --CEEEEEC-----CCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            346899999     999999999999999999  99999999997 7999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus       129 l~V~~a~~  136 (156)
T 3n9u_C          129 VDVRPATR  136 (156)
T ss_dssp             CEEEECCH
T ss_pred             eEEEEcCC
Confidence            99999986

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.62  E-value=9.8e-16  Score=133.57  Aligned_cols=86  Identities=16%  Similarity=0.222  Sum_probs=79.4

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ...+..+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..+
T Consensus         6 ~~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~   80 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQ-----IPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKT   80 (106)
T ss_dssp             CSCCCTTCEEEEEES-----CCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCC
T ss_pred             CCCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcc
Confidence            344556778899999     99999999999999999999999999987 699999999999999999999999999987


Q ss_pred             ---CCceEEEEEccC
Q psy3345          84 ---FSSRIKVEKCSN   95 (787)
Q Consensus        84 ---~~~~i~v~~~~~   95 (787)
                         .|+.|.|.+|.+
T Consensus        81 ~~~~g~~l~v~~a~~   95 (106)
T 2dgp_A           81 LPGMNRPIQVKPADS   95 (106)
T ss_dssp             CTTCSSCCEEEECCC
T ss_pred             cCCCCceEEEEECCc
Confidence               899999999987

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.62  E-value=7.3e-16  Score=138.89  Aligned_cols=86  Identities=22%  Similarity=0.354  Sum_probs=79.8

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~~G~afV~F~~~~~A~~Ai~~ln-g~~i~g~~l~  119 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-QSRRSRGFAFVYFENVDDAKEAKERAN-GMELDGRRIR  119 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCS-SSSCCCCEEEEEESCHHHHHHHHHHHT-TCCSSSSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCccceEEEEEECCHHHHHHHHHHhC-CCEECCEEEE
Confidence            34578999999999999999999999999999999999886 678999999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.++.
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998754

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.1e-15  Score=133.73  Aligned_cols=84  Identities=29%  Similarity=0.486  Sum_probs=77.2

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ......++|||+|||..+|+++|+++|++||.|.+|+|+.+   .+.++|||||+|.+.++|.+|+..|| +..+.|++|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~~~kg~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l   99 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN---ERGSKGFGFVTFENSADADRAREKLH-GTVVEGRKI   99 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCB---TTBCTTEEEEECCCSHHHHHHHHHHT-TCEETTEEC
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEEC---CCCCceEEEEEECCHHHHHHHHHHcC-CCEECCEEE
Confidence            33457899999999999999999999999999999999988   35589999999999999999999997 799999999


Q ss_pred             EEEEcccc
Q psy3345         760 VLEWAEEA  767 (787)
Q Consensus       760 ~v~~A~~~  767 (787)
                      .|+||.++
T Consensus       100 ~V~~a~~~  107 (109)
T 2err_A          100 EVNNATAR  107 (109)
T ss_dssp             EEEECCCS
T ss_pred             EEEECCCC
Confidence            99999875

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.62  E-value=3.6e-16  Score=126.81  Aligned_cols=74  Identities=22%  Similarity=0.357  Sum_probs=69.8

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      +|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|++|++ +|+..|+|+.|.|.+
T Consensus         1 ~l~v~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   74 (75)
T 2mss_A            1 KIFVGG-----LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEEC-----CCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEEC
T ss_pred             CEEEec-----CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEe
Confidence            467777     99999999999999999999999999988 79999999999999999999998 799999999999987


Q ss_pred             c
Q psy3345          93 C   93 (787)
Q Consensus        93 ~   93 (787)
                      |
T Consensus        75 A   75 (75)
T 2mss_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.62  E-value=1.4e-16  Score=173.98  Aligned_cols=172  Identities=16%  Similarity=0.247  Sum_probs=111.9

Q ss_pred             HHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEE--EEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhh-
Q psy3345         596 SIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG--FVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT-  672 (787)
Q Consensus       596 ~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~a--fV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~-  672 (787)
                      .|..+|.++|+|..+..+.........+....|++  |+.|....++..++..++.....++................. 
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~   87 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELK   87 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            37899999999987743322110000112223444  778877766655554333322221110000000000000000 


Q ss_pred             h--hhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC
Q psy3345         673 V--KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ  750 (787)
Q Consensus       673 ~--~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~  750 (787)
                      .  ..........+.++|||.|||+.+|+++|+++|+.||.|..|.|+.+. .+|.++|||||+|.+.++|..||..|| 
T Consensus        88 ~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~kG~aFV~F~~~e~A~~Ai~~ln-  165 (437)
T 3pgw_S           88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK-RSGKPRGYAFIEYEHERDMHSAYKHAD-  165 (437)
T ss_pred             hcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccC-CCCCccceEEEeeccHHHHHHHHHHcC-
Confidence            0  000011123466899999999999999999999999999999999885 589999999999999999999999997 


Q ss_pred             CeeecCceEEEEEcccccc
Q psy3345         751 STHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       751 ~~~~~Gr~l~v~~A~~~~~  769 (787)
                      +..|.|+.|.|.||.+...
T Consensus       166 g~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          166 GKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             CCEECCEEEEEEEeCCCCC
Confidence            7999999999999987553

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.62  E-value=1.4e-15  Score=141.58  Aligned_cols=83  Identities=12%  Similarity=0.302  Sum_probs=77.1

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcC--CeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G--~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..++|||+|||+.+|+++|+++|+.||  .|.+|+|+.+. .+|+++|||||+|.+.++|.+||..|| +..+.|+.|.|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~-~tg~skGfaFV~f~~~~~A~~Ai~~ln-g~~~~Gr~l~V  131 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENR-ANGQSKGYAEVVVASENSVHKLLELLP-GKVLNGEKVDV  131 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECT-TTCCEEEEEEEEESCHHHHHHHHHHST-TCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecC-CCCccceEEEEEECCHHHHHHHHHHcC-CCEECCeEeEE
Confidence            568999999999999999999999999  99999999885 689999999999999999999999997 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      .||.+..
T Consensus       132 ~~a~~~~  138 (156)
T 3n9u_C          132 RPATRQN  138 (156)
T ss_dssp             EECCHHH
T ss_pred             EEcCCCc
Confidence            9998754

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.62  E-value=2e-15  Score=131.89  Aligned_cols=82  Identities=33%  Similarity=0.479  Sum_probs=77.2

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~  101 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR--SGRSLGTADVHFERKADALKAMKQYN-GVPLDGRPMN  101 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT--TSCEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC--CCCcceEEEEEECCHHHHHHHHHHhC-CCEeCCcEEE
Confidence            34578999999999999999999999999999999999984  89999999999999999999999997 7999999999


Q ss_pred             EEEcc
Q psy3345         761 LEWAE  765 (787)
Q Consensus       761 v~~A~  765 (787)
                      |+||.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99985

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1e-15  Score=133.02  Aligned_cols=85  Identities=19%  Similarity=0.290  Sum_probs=78.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHh-cCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCee-ecCceE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKA-FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH-LYGRRL  759 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~-~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~-~~Gr~l  759 (787)
                      ..+.++|||.|||..+|+++|+++|+. ||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+..|+ +.. +.|++|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~--~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~~g~~l   82 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ--TGVSKGYGFVKFTDELEQKRALTECQ-GAVGLGSKPV   82 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT--TCCEEEEEEEEESCHHHHHHHHHHTT-TCCSSSSSCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC--CCCccceEEEEECCHHHHHHHHHHcc-CCcccCCEeE
Confidence            356789999999999999999999999 9999999999984  89999999999999999999999997 688 999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||.++..
T Consensus        83 ~v~~a~~~~~   92 (104)
T 2dhg_A           83 RLSVAIPKAS   92 (104)
T ss_dssp             CCCBCCCCCS
T ss_pred             EEEEccCCCc
Confidence            9999987654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.5e-15  Score=134.00  Aligned_cols=87  Identities=18%  Similarity=0.277  Sum_probs=80.0

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCee--------EEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCe
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELK--------FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST  752 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~--------~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~  752 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.        .|+|+.+. .+|.++|||||+|.+.++|.+|+..|| +.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~   88 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK-ETGKPKGDATVSYEDPPTAKAAVEWFD-GK   88 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT-TTCSBCSEEEEEBSSHHHHHHHHHHHT-TC
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeC-CCCCeeeEEEEEECCHHHHHHHHHHcC-CC
Confidence            345789999999999999999999999999999        59999885 689999999999999999999999997 79


Q ss_pred             eecCceEEEEEcccccc
Q psy3345         753 HLYGRRLVLEWAEEADN  769 (787)
Q Consensus       753 ~~~Gr~l~v~~A~~~~~  769 (787)
                      .+.|++|+|+||.++..
T Consensus        89 ~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             ccCCCEEEEEECCCCCC
Confidence            99999999999997764

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=1.7e-15  Score=130.35  Aligned_cols=81  Identities=15%  Similarity=0.252  Sum_probs=72.4

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-CeeecCceEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-STHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-~~~~~Gr~l~  760 (787)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|+++       ||||||+|.+.++|.+|+..|++ +..+.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            457899999999999999999999999999999998764       79999999999999999999863 3459999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.++..
T Consensus        85 V~~a~~~~~   93 (104)
T 1wex_A           85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCccc
Confidence            999986653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2.3e-15  Score=127.14  Aligned_cols=82  Identities=22%  Similarity=0.379  Sum_probs=76.4

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||+|||..+|+++|+++|+.| .|.+|+|+++  .+|+++|||||+|.+.++|.+|+. || +..+.|+.|.|
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~--~~g~~~g~afV~f~~~~~a~~A~~-~~-g~~~~gr~i~v   81 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN--AHGNKTGYIFVDFSNEEEVKQALK-CN-REYMGGRYIEV   81 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC--TTSCEEEEEEEECSSHHHHHHHHH-SC-SEEETTEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC--CCCCCceEEEEEECCHHHHHHHHH-hC-CceeCCcEEEE
Confidence            4567899999999999999999999999 8999999998  589999999999999999999999 96 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      .||.++.
T Consensus        82 ~~a~~~~   88 (91)
T 2dgw_A           82 FREKSGP   88 (91)
T ss_dssp             EEESSCC
T ss_pred             EECCcCC
Confidence            9998653

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.61  E-value=4.3e-16  Score=134.05  Aligned_cols=84  Identities=25%  Similarity=0.507  Sum_probs=75.1

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||+|||..+|+++|+++|+.|| |.+|+|+++...+|+++|||||+|.+.++|.+|+ .|+ +..+.|+.|.|
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~-g~~~~g~~l~V   92 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-EESLGNRRIRV   92 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTT-TCCBTTBCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcC-CCEECCeEEEE
Confidence            45679999999999999999999999999 9999999885347999999999999999999999 896 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      +||.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9998764

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.61  E-value=6e-16  Score=125.51  Aligned_cols=75  Identities=23%  Similarity=0.402  Sum_probs=70.8

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      +|||+|||..+|+++|+++|++||.|.+++++.+. .+|+++|||||+|.+.++|.+|++ ++ +..+.|++|.|.||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~a~~-~~-~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK-TTNRHRGFGFVTFESEDIVEKVCE-IH-FHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCS-SSTTSCBEEEEECSCHHHHHHHHS-SS-CCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCCcCcEEEEEECCHHHHHHHHH-CC-CCEECCEEEEEEeC
Confidence            48999999999999999999999999999999885 589999999999999999999998 86 79999999999997

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=1.3e-15  Score=129.82  Aligned_cols=78  Identities=28%  Similarity=0.385  Sum_probs=71.6

Q ss_pred             CCcccceEEEecCcccCCCc-cCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccC--ccC
Q psy3345           8 PVVPRNHISLLDLDEVEFIY-KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT--YVF   84 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~--~~~   84 (787)
                      ..-|+..|+|.|     ||+ .+||+||+++|+.||.|.+|.|+.+     +|||||.|.+.++|..|++.||+.  .|.
T Consensus        11 ~~~p~~~l~V~n-----Lp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~   80 (102)
T 1x4d_A           11 RVETRRVVHIMD-----FQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVF   80 (102)
T ss_dssp             CCCCCCEEEEES-----CCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCCCEEEEeC-----CCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceEC
Confidence            344788899999     999 9999999999999999999999875     589999999999999999999964  599


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      ||.|.|.+|++
T Consensus        81 Gr~l~V~~a~~   91 (102)
T 1x4d_A           81 GKPVRVHLSQK   91 (102)
T ss_dssp             TEECEEEEECC
T ss_pred             CcEEEEEECCC
Confidence            99999999986

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.1e-15  Score=136.19  Aligned_cols=80  Identities=20%  Similarity=0.268  Sum_probs=74.8

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|++|
T Consensus        38 ~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  112 (118)
T 2khc_A           38 PEGCNLFIYH-----LPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL  112 (118)
T ss_dssp             CCSEEEEEEC-----SCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEEC
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3457799999     99999999999999999999999999987 69999999999999999999999999999999999


Q ss_pred             EEEEcc
Q psy3345          89 KVEKCS   94 (787)
Q Consensus        89 ~v~~~~   94 (787)
                      .|.+++
T Consensus       113 ~V~~ak  118 (118)
T 2khc_A          113 KVQLKK  118 (118)
T ss_dssp             CEEEC-
T ss_pred             EEEecC
Confidence            999874

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.2e-15  Score=135.89  Aligned_cols=82  Identities=21%  Similarity=0.403  Sum_probs=76.4

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|++||.|.+++|+++. .+|+++|||||+|.+.++|.+|+..|| +..+.|++|+|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~V  114 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK-QTSLSKCFGFVSFDNPDSAQVAIKAMN-GFQVGTKRLKV  114 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCS-SSSCCCCEEEEEEESSHHHHHHHHHCC-CCEETTEECCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-CCCCcCcEEEEEECCHHHHHHHHHHcC-CCEECCEEEEE
Confidence            4567999999999999999999999999999999999885 679999999999999999999999997 79999999999


Q ss_pred             EEcc
Q psy3345         762 EWAE  765 (787)
Q Consensus       762 ~~A~  765 (787)
                      +||+
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9985

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3.7e-16  Score=130.18  Aligned_cols=81  Identities=14%  Similarity=0.153  Sum_probs=75.1

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..++..|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus         2 ~~~~~~l~v~n-----lp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   76 (85)
T 1x4e_A            2 SSGSSGLYIRG-----LQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQM   76 (85)
T ss_dssp             CCCCCEEEEES-----CCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEES
T ss_pred             CCCCcEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEE
Confidence            45678899999     99999999999999999999999999987 7999999999999999999999999999999999


Q ss_pred             EEEEEcc
Q psy3345          88 IKVEKCS   94 (787)
Q Consensus        88 i~v~~~~   94 (787)
                      |+|.+++
T Consensus        77 ~~~~~~~   83 (85)
T 1x4e_A           77 AKQSGPS   83 (85)
T ss_dssp             CCSSCCC
T ss_pred             EeecCCC
Confidence            9876543

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.61  E-value=3.6e-15  Score=124.75  Aligned_cols=80  Identities=21%  Similarity=0.492  Sum_probs=74.9

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++ +++..+.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            3567899999999999999999999999999999999998899999999999999999999996 688899999999987


Q ss_pred             C
Q psy3345         413 G  413 (787)
Q Consensus       413 ~  413 (787)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1e-15  Score=133.04  Aligned_cols=80  Identities=25%  Similarity=0.431  Sum_probs=76.6

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      +...|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|.|+.|.
T Consensus         7 ~~~~l~V~n-----lp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (104)
T 1p1t_A            7 SLRSVFVGN-----IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             HHSCEEEES-----CCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CccEEEEeC-----CCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            567899999     99999999999999999999999999987 799999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|.+
T Consensus        82 v~~a~~   87 (104)
T 1p1t_A           82 VDNAAS   87 (104)
T ss_dssp             EEETTC
T ss_pred             EEeCCC
Confidence            999986

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.61  E-value=5e-16  Score=140.92  Aligned_cols=86  Identities=22%  Similarity=0.409  Sum_probs=79.0

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeE--EEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCe----e
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST----H  753 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~--v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~----~  753 (787)
                      ....+.++|||+|||+.+|+++|+++|++||.|..  |+|+++. .+|+++|||||+|.+. +|.+|+..|| +.    .
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~-~tg~~rG~aFV~f~~~-~a~~Ai~~l~-g~~~~~~   94 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDK-QTQLNRGFAFIQLSTI-EAAQLLQILQ-ALHPPLT   94 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCS-SSSSBCSCEEEECCHH-HHHHHHHHHT-TCCCSCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcC-CCCCcceEEEEEECCH-HHHHHHHHhc-CCCCCcc
Confidence            33467889999999999999999999999999977  9999985 6899999999999999 9999999997 68    9


Q ss_pred             ecCceEEEEEccccc
Q psy3345         754 LYGRRLVLEWAEEAD  768 (787)
Q Consensus       754 ~~Gr~l~v~~A~~~~  768 (787)
                      +.||+|.|+||.+..
T Consensus        95 ~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           95 IDGKTINVEFAKGSK  109 (131)
T ss_dssp             GGGCCCCCEECCCSC
T ss_pred             CCCEEEEEEECCCCC
Confidence            999999999998764

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2.3e-15  Score=133.51  Aligned_cols=87  Identities=24%  Similarity=0.431  Sum_probs=79.1

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ....+.++|||.|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..++ + .+.|++|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~Ai~~~~-~-~~~g~~l   88 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR-QTGKSRGYGFVTMADRAAAERACKDPN-P-IIDGRKA   88 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS-SSCCCCSEEEEEESSHHHHHHHHTCSS-C-EETTEEC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcC-CCCccceEEEEEECCHHHHHHHHHhCC-C-cCCCEEE
Confidence            344578999999999999999999999999999999999985 579999999999999999999999997 5 8999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||.+...
T Consensus        89 ~V~~a~~~~~   98 (116)
T 2cqd_A           89 NVNLAYLGAK   98 (116)
T ss_dssp             EEEESTTTCC
T ss_pred             EEEEcccCCC
Confidence            9999976543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=3.1e-15  Score=132.25  Aligned_cols=85  Identities=25%  Similarity=0.379  Sum_probs=78.4

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+..|| +..+.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~--~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   87 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK--DGKSRGIGTVTFEQSIEAVQAISMFN-GQLLFDRPMH   87 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT--TCSEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC--CCCeeeEEEEEECCHHHHHHHHHHhC-CCEeCCCEEE
Confidence            34567899999999999999999999999999999999984  69999999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.+..
T Consensus        88 v~~a~~~~   95 (114)
T 2do0_A           88 VKMDERAL   95 (114)
T ss_dssp             EEECSCCC
T ss_pred             EEEcccCC
Confidence            99998543

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.61  E-value=2.1e-15  Score=135.95  Aligned_cols=88  Identities=24%  Similarity=0.454  Sum_probs=80.3

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ....+.++|||.|||..+|+++|+++|+.||.|.+|.|+.+. .+|.++|||||+|.+.++|.+|+..|| +..+.|+.|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l   94 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAAMEGLN-GQDLMGQPI   94 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT-TTSSBCSCEEEEESSHHHHHHHHHHHT-TCBSSSSBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCccceEEEEEECCHHHHHHHHHHhC-CCeeCCeEE
Confidence            344567899999999999999999999999999999999885 589999999999999999999999997 799999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||.++..
T Consensus        95 ~v~~a~~~~~  104 (126)
T 3ex7_B           95 SVDWCFVRGP  104 (126)
T ss_dssp             EEEESEESSS
T ss_pred             EEEEecCCCC
Confidence            9999986553

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3.5e-15  Score=130.70  Aligned_cols=82  Identities=23%  Similarity=0.409  Sum_probs=75.3

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|..|+|+.+    +.++|||||+|.+.++|.+|++.|| +..+.|++|.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~V   93 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR----RGGPPFAFVEFEDPRDAEDAVYGRD-GYDYDGYRLRV   93 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS----SSSSCCEEEEESCHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC----CCCCcEEEEEECCHHHHHHHHHHcC-CCEECCeEEEE
Confidence            456789999999999999999999999999999999664    5589999999999999999999997 69999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      +||++..
T Consensus        94 ~~a~~~~  100 (109)
T 1x4a_A           94 EFPRSGR  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EEcccCC
Confidence            9998754

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.3e-15  Score=133.15  Aligned_cols=83  Identities=16%  Similarity=0.346  Sum_probs=76.8

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ....+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ ++++|||||.|.+.++|.+|++.||+..|+|+
T Consensus        24 ~~~~~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   97 (109)
T 2err_A           24 ENKSQPKRLHVSN-----IPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADRAREKLHGTVVEGR   97 (109)
T ss_dssp             SCTTCCCEEEEES-----CCTTCCHHHHHHHGGGTCCCSCEEECCBT-TBCTTEEEEECCCSHHHHHHHHHHTTCEETTE
T ss_pred             cCCCCCCEEEEEC-----CCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3445677899999     99999999999999999999999999986 45999999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|++
T Consensus        98 ~l~V~~a~~  106 (109)
T 2err_A           98 KIEVNNATA  106 (109)
T ss_dssp             ECEEEECCC
T ss_pred             EEEEEECCC
Confidence            999999986

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=1.5e-15  Score=133.40  Aligned_cols=85  Identities=20%  Similarity=0.274  Sum_probs=77.8

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHH---HHhhccCceEEEEEEecCC----CCcceEEEEEecCHHHHHHHHHHh
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLK---AKFEEKGTVTDVQLKYTTE----GKFRRFAFIGYHREDQAQAALDYF   78 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~---~~f~~~g~i~~~~~~~~~~----g~~~g~afv~f~~~~~a~~a~~~~   78 (787)
                      ....+++++|+|.|     ||+++|+++|+   ++|+.||.|.+|.|+.++.    ++++|||||+|.+.++|++||+.|
T Consensus         9 ~~r~~~~~~l~V~n-----Lp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~l   83 (111)
T 2cpi_A            9 SVRVVQKNLVFVVG-----LSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCV   83 (111)
T ss_dssp             CCCCCCSSCEEEEE-----ECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHH
T ss_pred             cccccCCCEEEEEC-----CCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHh
Confidence            34566788899999     99999999999   9999999999999998763    356799999999999999999999


Q ss_pred             ccCccCCceEEEEEccC
Q psy3345          79 NNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        79 ~~~~~~~~~i~v~~~~~   95 (787)
                      |+..|+||.|.|.+|.+
T Consensus        84 ng~~~~gr~l~V~~a~~  100 (111)
T 2cpi_A           84 NNVVVDGRTLKASLGTT  100 (111)
T ss_dssp             TTEEETTEEEEEESCCC
T ss_pred             CCCEECCEEEEEEeccc
Confidence            99999999999999987

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.8e-15  Score=131.58  Aligned_cols=81  Identities=17%  Similarity=0.266  Sum_probs=76.5

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..+..+|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||+|.+.++|.+||+. |+..|+|+.
T Consensus        13 ~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   86 (105)
T 2dh8_A           13 ADEIGKLFVGG-----LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRN   86 (105)
T ss_dssp             SSSSSEECCBS-----CCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEE
Confidence            45667788888     99999999999999999999999999986 799999999999999999999999 999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus        87 l~V~~a~~   94 (105)
T 2dh8_A           87 IDPKPCTP   94 (105)
T ss_dssp             EBCCCSCC
T ss_pred             EEEEEccC
Confidence            99999987

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=9.7e-16  Score=135.27  Aligned_cols=85  Identities=18%  Similarity=0.257  Sum_probs=78.2

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCe-eEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I-~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ..+.++|||+|||+.+|+++|+++|+.||.| .+|+|+.+.  +|+++|||||+|.+.++|.+||.. | +..|.|+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~--~g~~~G~afV~F~~~~~a~~Al~~-~-~~~~~gr~i~   87 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN--NGQGLGQALVQFKNEDDARKSERL-H-RKKLNGREAF   87 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT--TSSCSSCEEEECSSHHHHHHHGGG-C-SEEETTEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC--CCCcceEEEEEECCHHHHHHHHHh-C-CCccCCeEEE
Confidence            4567899999999999999999999999999 899999984  899999999999999999999987 5 7999999999


Q ss_pred             EEEccccccH
Q psy3345         761 LEWAEEADNV  770 (787)
Q Consensus       761 v~~A~~~~~~  770 (787)
                      |.||.+++..
T Consensus        88 v~~a~~~~~~   97 (114)
T 2cpy_A           88 VHVVTLEDMR   97 (114)
T ss_dssp             EEEECHHHHH
T ss_pred             EEECCHHHHH
Confidence            9999876644

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.60  E-value=5.8e-16  Score=133.22  Aligned_cols=81  Identities=22%  Similarity=0.376  Sum_probs=73.1

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC--CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT--EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      +..+..+|+|.|     ||+++|+++|+++|+.|| |.+|+|+.++  +|+++|||||.|.+.++|.+|+ .||+..|+|
T Consensus        15 ~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g   87 (100)
T 2j76_E           15 PKSPPYTAFLGN-----LPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN   87 (100)
T ss_dssp             -----CEEEESC-----CSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTT
T ss_pred             CCCCCcEEEEeC-----CCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECC
Confidence            445677899999     999999999999999999 9999999987  7999999999999999999999 899999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|++
T Consensus        88 ~~l~V~~a~~   97 (100)
T 2j76_E           88 RRIRVDVADQ   97 (100)
T ss_dssp             BCCCCEECCC
T ss_pred             eEEEEEeccC
Confidence            9999999986

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.60  E-value=1.8e-15  Score=131.31  Aligned_cols=81  Identities=14%  Similarity=0.146  Sum_probs=75.2

Q ss_pred             CcccceEEEecCcccCCCccC------CHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCc
Q psy3345           9 VVPRNHISLLDLDEVEFIYKI------TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY   82 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~   82 (787)
                      ...+++|+|.|     ||+.+      |+++|+++|+.||.|.+|.|+ ..+|+++|||||.|.+.++|.+|+..|||..
T Consensus        12 ~~~~~~l~V~n-----Lp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~   85 (105)
T 2nlw_A           12 DGIDSVIVVDN-----VPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYK   85 (105)
T ss_dssp             CSCCSEEEEES-----CCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEE
T ss_pred             CCCCCEEEEeC-----CCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcc
Confidence            33467899999     99999      889999999999999999998 4589999999999999999999999999999


Q ss_pred             cCCc-eEEEEEccC
Q psy3345          83 VFSS-RIKVEKCSN   95 (787)
Q Consensus        83 ~~~~-~i~v~~~~~   95 (787)
                      |+|| .|.|.+|..
T Consensus        86 ~~g~~~l~V~~a~~   99 (105)
T 2nlw_A           86 LDKQHTFRVNLFTD   99 (105)
T ss_dssp             CSTTCEEEEECSCC
T ss_pred             cCCCceEEEEEcch
Confidence            9999 999999975

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.60  E-value=4e-15  Score=125.14  Aligned_cols=80  Identities=30%  Similarity=0.541  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP  415 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  415 (787)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+ .|+|..+.|+.|.|.++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            468999999999999999999999999999999999889999999999999999999999 8999999999999999875


Q ss_pred             C
Q psy3345         416 K  416 (787)
Q Consensus       416 ~  416 (787)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.60  E-value=2.1e-15  Score=135.97  Aligned_cols=84  Identities=21%  Similarity=0.355  Sum_probs=78.6

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      +..+...|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|+
T Consensus        18 ~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           18 RSVEGWILFVTG-----VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             CCSSSEEEEEES-----CCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            344566899999     99999999999999999999999999987 899999999999999999999999999999999


Q ss_pred             eEEEEEccCC
Q psy3345          87 RIKVEKCSNL   96 (787)
Q Consensus        87 ~i~v~~~~~~   96 (787)
                      .|.|.+|.+.
T Consensus        93 ~l~v~~a~~~  102 (126)
T 3ex7_B           93 PISVDWCFVR  102 (126)
T ss_dssp             BCEEEESEES
T ss_pred             EEEEEEecCC
Confidence            9999999873

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.60  E-value=2.3e-15  Score=131.53  Aligned_cols=85  Identities=22%  Similarity=0.381  Sum_probs=75.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|+.||.|.+|+|+++. .+|+++|||||+|.+.++|.+|+..+  +..+.|+.|.|
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~tg~~kg~afV~f~~~~~A~~Ai~~~--~~~l~g~~l~V   98 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP-LTKRSRGFGFVTFMDQAGVDKVLAQS--RHELDSKTIDP   98 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCT-TTCCCTTCEEEEESSHHHHHHHHHSS--CEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECC-CCCCcCcEEEEEECCHHHHHHHHHHC--CCcCCCEEEEE
Confidence            3467899999999999999999999999999999999985 67999999999999999999999986  39999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      .||.++..
T Consensus        99 ~~a~~~~~  106 (109)
T 2rs2_A           99 KVAFPRRA  106 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987653

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=1.1e-15  Score=131.02  Aligned_cols=84  Identities=23%  Similarity=0.298  Sum_probs=76.6

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||.|||..+|+++|+++|+.||.|..+.++.+. .+|+++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~-~~g~~~g~afV~f~~~~~a~~Ai~~l~-g~~~~g~~l~V   89 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLN-DRPIGSRKVKL   89 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTT-TCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEEC-CCCCeeeEEEEEECCHHHHHHHHHHhC-CCeeCCeEEEE
Confidence            3456899999999999999999999999999888777764 688999999999999999999999997 69999999999


Q ss_pred             EEcccc
Q psy3345         762 EWAEEA  767 (787)
Q Consensus       762 ~~A~~~  767 (787)
                      +||...
T Consensus        90 ~~a~~~   95 (98)
T 2cqp_A           90 VLGSGP   95 (98)
T ss_dssp             EESSCS
T ss_pred             EEcCCC
Confidence            999754

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=8.4e-16  Score=138.01  Aligned_cols=83  Identities=19%  Similarity=0.248  Sum_probs=74.8

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEE-ecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLK-YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~-~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .|..+...|+|.|     ||+++|++||+++|+.||.|.++.++ .+.+|+++|||||.|.+.++|.+||+ ||+..|+|
T Consensus        20 ~~~~~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g   93 (124)
T 1wel_A           20 SPHEAGFCVYLKG-----LPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGN   93 (124)
T ss_dssp             SCCCCCCEEEEEC-----CCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT
T ss_pred             CCCCCCcEEEEeC-----CCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECC
Confidence            4555667899999     99999999999999999999884444 45589999999999999999999999 89999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      |+|.|.+|.+
T Consensus        94 r~i~V~~a~~  103 (124)
T 1wel_A           94 RFIQVHPITK  103 (124)
T ss_dssp             SCBEEEEECH
T ss_pred             cEEEEEECCH
Confidence            9999999986

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.60  E-value=1.1e-15  Score=132.83  Aligned_cols=80  Identities=21%  Similarity=0.188  Sum_probs=73.1

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccC-ceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKG-TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ++....+|+|.|     ||+++|++||+++|+.|| .|..|.|+.+   +++|||||.|.+.++|++||+.||+..|+||
T Consensus        24 ~p~~~~~l~Vgn-----Lp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr   95 (111)
T 2jvr_A           24 LPAKRYRITMKN-----LPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGS   95 (111)
T ss_dssp             -CCCCEEEEEEC-----SSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCCCEEEEEC-----CCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            555677899999     999999999999999999 8999988643   5899999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|++++.
T Consensus        96 ~i~V~~a~~  104 (111)
T 2jvr_A           96 VITVERDDN  104 (111)
T ss_dssp             EEEEEESCC
T ss_pred             EEEEEECCC
Confidence            999999975

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=2.5e-15  Score=132.59  Aligned_cols=81  Identities=21%  Similarity=0.304  Sum_probs=76.7

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceE--------EEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVT--------DVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      .+..+|+|.|     ||+.+|+++|+++|+.||.|.        .|+|+.++ +|+++|||||.|.+.++|.+||+.||+
T Consensus        13 ~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   87 (113)
T 2cpe_A           13 SDNSAIYVQG-----LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG   87 (113)
T ss_dssp             CCCCEEEEEC-----CCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEcC-----CCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCC
Confidence            3567899999     999999999999999999998        79999985 799999999999999999999999999


Q ss_pred             CccCCceEEEEEccC
Q psy3345          81 TYVFSSRIKVEKCSN   95 (787)
Q Consensus        81 ~~~~~~~i~v~~~~~   95 (787)
                      ..|.|+.|.|.++++
T Consensus        88 ~~~~g~~l~V~~a~~  102 (113)
T 2cpe_A           88 KDFQGSKLKVSLARK  102 (113)
T ss_dssp             CEETTEECEEECSSC
T ss_pred             CccCCCEEEEEECCC
Confidence            999999999999987

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.60  E-value=2.7e-16  Score=142.63  Aligned_cols=79  Identities=15%  Similarity=0.191  Sum_probs=73.5

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .+...|+|.|     |||++||+||+++|+.|| |.+|+|+++++|+++|||||+|.+.++|++|| .+|+..|+||+|+
T Consensus        44 ~~~~~lfV~n-----Lp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~  116 (139)
T 2hgn_A           44 TTGHCVHMRG-----LPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIE  116 (139)
T ss_dssp             -CCCCEECCS-----CCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCC
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEE
Confidence            4556799999     999999999999999999 67999999999999999999999999999999 6799999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |..+.+
T Consensus       117 V~~a~~  122 (139)
T 2hgn_A          117 LFLNST  122 (139)
T ss_dssp             CEECCC
T ss_pred             EEECCC
Confidence            999886

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=5.3e-15  Score=128.11  Aligned_cols=85  Identities=26%  Similarity=0.520  Sum_probs=77.6

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+..   +..+.|++|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A~~~---~~~~~g~~l~   86 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL-KTGHSKGFGFVRFTEYETQVKVMSQ---RHMIDGRWCD   86 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHHHHS---CEEETTEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecC-CCCCccceEEEEECCHHHHHHHHHc---CCeeCCeEEE
Confidence            34567899999999999999999999999999999999985 5799999999999999999999983   5799999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |.||.++..
T Consensus        87 v~~a~~~~~   95 (103)
T 2cqg_A           87 CKLPNSKQS   95 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EEecCCCCc
Confidence            999997764

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=5.9e-15  Score=127.82  Aligned_cols=82  Identities=17%  Similarity=0.246  Sum_probs=75.2

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .+..+|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+||+.  +..|+|+.|
T Consensus        13 ~~~~~l~v~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~l   85 (103)
T 2cqg_A           13 QKTSDLIVLG-----LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWC   85 (103)
T ss_dssp             CCCCCEEEES-----CCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEE
T ss_pred             CCCCEEEEEc-----CCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCeEE
Confidence            4567799999     99999999999999999999999999987 699999999999999999999994  679999999


Q ss_pred             EEEEccCCCC
Q psy3345          89 KVEKCSNLGD   98 (787)
Q Consensus        89 ~v~~~~~~~~   98 (787)
                      .|.++.+...
T Consensus        86 ~v~~a~~~~~   95 (103)
T 2cqg_A           86 DCKLPNSKQS   95 (103)
T ss_dssp             EEECCCTTCC
T ss_pred             EEEecCCCCc
Confidence            9999987433

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.4e-15  Score=132.29  Aligned_cols=86  Identities=21%  Similarity=0.320  Sum_probs=79.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+.. + +..+.|+.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~a~~~-~-~~~~~g~~l~   88 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDK-TTNQSRGFGFVKFKDPNCVGTVLAS-R-PHTLDGRNID   88 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECS-SSCCEEEEEEEEESSTTHHHHHHHH-C-SEEETTEEEB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC-CCCCcceEEEEEECCHHHHHHHHHh-C-CCeECCEEEE
Confidence            34577999999999999999999999999999999999985 6899999999999999999999998 6 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.++..
T Consensus        89 V~~a~~~~~   97 (105)
T 2dh8_A           89 PKPCTPRGM   97 (105)
T ss_dssp             CCCSCCSSC
T ss_pred             EEEccCCCC
Confidence            999997764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.60  E-value=7e-15  Score=135.06  Aligned_cols=82  Identities=18%  Similarity=0.295  Sum_probs=77.5

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..|.|+.
T Consensus        39 ~~~~~~l~V~n-----Lp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  113 (139)
T 1u6f_A           39 PDVLRNLMVNY-----IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR  113 (139)
T ss_dssp             TTTTSEEEEES-----CSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34567899999     99999999999999999999999999987 6899999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|++
T Consensus       114 l~v~~a~~  121 (139)
T 1u6f_A          114 LKVALAAS  121 (139)
T ss_dssp             EEEEESSC
T ss_pred             EEEEECCC
Confidence            99999987

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=7.3e-16  Score=138.40  Aligned_cols=92  Identities=21%  Similarity=0.271  Sum_probs=79.4

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      +....++|||+|||+.+|+++|+++|+.||.|.++.++.+. .+|+++|||||+|.+.++|.+||. || +..|.|+.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~-~~g~~~G~afV~F~~~~~a~~Al~-~~-g~~~~gr~i~   97 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG-PNGKATGEGFVEFRNEADYKAALC-RH-KQYMGNRFIQ   97 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC-TTSSEEEEEEEEBSSSHHHHHHHT-SC-SBCSTTSCBE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEEC-CCCCCCeEEEEEECCHHHHHHHHH-hC-CCeECCcEEE
Confidence            34567999999999999999999999999999885444442 589999999999999999999999 86 7999999999


Q ss_pred             EEEccccccHHHHHH
Q psy3345         761 LEWAEEADNVEDIRK  775 (787)
Q Consensus       761 v~~A~~~~~~~~~~~  775 (787)
                      |.+|.+++..+.+..
T Consensus        98 V~~a~~~~~~~~~~~  112 (124)
T 1wel_A           98 VHPITKKGMLEKIDM  112 (124)
T ss_dssp             EEEECHHHHHHHHHH
T ss_pred             EEECCHHHHHHHHHH
Confidence            999998876544443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.59  E-value=3e-15  Score=130.82  Aligned_cols=81  Identities=16%  Similarity=0.177  Sum_probs=73.5

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ..+..+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.+ +..|+|+.
T Consensus        22 ~~~~~~lfV~n-----Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~   95 (109)
T 2rs2_A           22 GSSGCKMFIGG-----LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKT   95 (109)
T ss_dssp             ----CCEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEE
Confidence            34567899999     99999999999999999999999999987 6999999999999999999999995 59999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.++.+
T Consensus        96 l~V~~a~~  103 (109)
T 2rs2_A           96 IDPKVAFP  103 (109)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999986

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.59  E-value=5.2e-15  Score=132.92  Aligned_cols=85  Identities=31%  Similarity=0.443  Sum_probs=79.0

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...++++|||+|||..+|+++|+++|+.||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+..|| +..+.|++|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~  107 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR--SGRSLGTADVHFERRADALKAMKQYK-GVPLDGRPMD  107 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS--SSSCCSEEEEEESSHHHHHHHHHHHT-TEESSSCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC--CCCEeeEEEEEECCHHHHHHHHHHcC-CCEECCcEEE
Confidence            34567899999999999999999999999999999999984  89999999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.+..
T Consensus       108 V~~a~~~~  115 (124)
T 2kt5_A          108 IQLVASQI  115 (124)
T ss_dssp             EEEECCTT
T ss_pred             EEEeCCCC
Confidence            99998654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=1.1e-15  Score=124.78  Aligned_cols=74  Identities=18%  Similarity=0.240  Sum_probs=70.5

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      +|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|++.+| ..++|+.|.|.+
T Consensus         2 ~l~v~n-----lp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~   75 (77)
T 1uaw_A            2 KMFIGG-----LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKV   75 (77)
T ss_dssp             CEEEES-----CCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEE
T ss_pred             EEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEe
Confidence            578888     99999999999999999999999999987 69999999999999999999999999 999999999998


Q ss_pred             c
Q psy3345          93 C   93 (787)
Q Consensus        93 ~   93 (787)
                      |
T Consensus        76 a   76 (77)
T 1uaw_A           76 A   76 (77)
T ss_dssp             C
T ss_pred             c
Confidence            7

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.59  E-value=2.2e-15  Score=128.96  Aligned_cols=84  Identities=20%  Similarity=0.419  Sum_probs=76.6

Q ss_pred             CCCCCEEEEecCCccCcHHHHH----HHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVE----ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~----~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      ..++++|||+|||..+|+++|+    ++|++||.|.+|++++    +|.++|||||+|.+.++|..|+..|| +..+.|+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~----~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~   79 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR----SLKMRGQAFVIFKEVSSATNALRSMQ-GFPFYDK   79 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH----HHHHTTCEEEEESSHHHHHHHHHHHT-TCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc----CCCcCcEEEEEeCCHHHHHHHHHHhC-CCEECCc
Confidence            3578999999999999999999    9999999999999974    46789999999999999999999997 7999999


Q ss_pred             eEEEEEccccccH
Q psy3345         758 RLVLEWAEEADNV  770 (787)
Q Consensus       758 ~l~v~~A~~~~~~  770 (787)
                      +|.|+||.++...
T Consensus        80 ~l~v~~a~~~~~~   92 (97)
T 1nu4_A           80 PMRIQYAKTDSDI   92 (97)
T ss_dssp             ECEEEECSSCCTH
T ss_pred             EEEEEEccCCCcc
Confidence            9999999987754

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=4.1e-15  Score=130.33  Aligned_cols=84  Identities=17%  Similarity=0.145  Sum_probs=76.9

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCc-eEEEEEE-ecC-CCCcceEEEEEecCHHHHHHHHHHhc--cCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGT-VTDVQLK-YTT-EGKFRRFAFIGYHREDQAQAALDYFN--NTY   82 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~-i~~~~~~-~~~-~g~~~g~afv~f~~~~~a~~a~~~~~--~~~   82 (787)
                      .+.+..+|+|.|     ||+.+|+++|+++|+.||. |.+|.|+ .++ +|+++|||||.|.+.++|.+|++.||  +..
T Consensus         4 ~s~~~~~l~V~n-----Lp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~   78 (109)
T 2dis_A            4 GSSGNCRLFIGG-----IPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQ   78 (109)
T ss_dssp             CCCCSEEEEEEC-----CCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSC
T ss_pred             cccCCCEEEEeC-----CCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCce
Confidence            345678899999     9999999999999999998 9999998 565 58999999999999999999999997  589


Q ss_pred             cCCceEEEEEccCC
Q psy3345          83 VFSSRIKVEKCSNL   96 (787)
Q Consensus        83 ~~~~~i~v~~~~~~   96 (787)
                      +.|+.|.|.+|++.
T Consensus        79 ~~g~~l~V~~a~~~   92 (109)
T 2dis_A           79 LWGHQIAVDWAEPE   92 (109)
T ss_dssp             BTTBCCEEEESCSS
T ss_pred             ecCCeEEEEEcCCC
Confidence            99999999999973

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=2.7e-15  Score=131.71  Aligned_cols=85  Identities=20%  Similarity=0.271  Sum_probs=77.0

Q ss_pred             CCCCCEEEEecCCccCcHHHHH---HHHHhcCCeeEEEeccccCC---CCCCceEEEEEecCHHHHHHHHHHhcCCeeec
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVE---ELFKAFGELKFVRLPKKMVG---SGLHRGFGFVEFITKNEAKRAMKALCQSTHLY  755 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~---~~F~~~G~I~~v~i~~~~~~---~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~  755 (787)
                      ..+.++|||.|||+.+|+++|+   ++|++||.|..|+|+++. .   .++++|||||+|.+.++|.+|+..|| +..+.
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~-~~~~~~~~~G~afV~f~~~~~A~~Ai~~ln-g~~~~   89 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNST-SYAGSQGPSASAYVTYIRSEDALRAIQCVN-NVVVD   89 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCS-SCCSSSCCCEEEEEEESSHHHHHHHHHHHT-TEEET
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCC-CcCccCCCCeEEEEEECcHHHHHHHHHHhC-CCEEC
Confidence            3467899999999999999999   999999999999998874 3   23667999999999999999999997 79999


Q ss_pred             CceEEEEEccccc
Q psy3345         756 GRRLVLEWAEEAD  768 (787)
Q Consensus       756 Gr~l~v~~A~~~~  768 (787)
                      |++|.|+||.++.
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999999775

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=1.8e-15  Score=130.63  Aligned_cols=100  Identities=17%  Similarity=0.319  Sum_probs=83.6

Q ss_pred             CeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Q psy3345         581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK  660 (787)
Q Consensus       581 ~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~  660 (787)
                      ++|||+|||+++++++|+++|++||.|.++.+..+          ++|||||+|.+.++|.+|+..|||..++|+.|.|.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----------~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   70 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----------PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE   70 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----------SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----------CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEE
Confidence            47999999999999999999999999999999864          57999999999999999999999999999999999


Q ss_pred             ecCccccchhhhhhhccccccCCCCCEEEEecCC
Q psy3345         661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP  694 (787)
Q Consensus       661 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp  694 (787)
                      ++.......    .............+|||.||+
T Consensus        71 ~a~~~~~~~----~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           71 LSTGMPRRS----RFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             ESSSCCCSS----CCCSCCCSCCCCSCCCSCCCC
T ss_pred             EccCCCCcc----cCCCCCccccCCCceecCCCC
Confidence            998765411    111111223447789999996

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=5e-15  Score=127.75  Aligned_cols=81  Identities=22%  Similarity=0.307  Sum_probs=74.5

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ...++.+|+|.|     ||+++|+++|+++|+.||.|   +|+.+.+|+++|||||.|.+.++|++|++.||+..|.|+.
T Consensus        11 ~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   82 (101)
T 2fc9_A           11 WSGESKTLVLSN-----LSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRA   82 (101)
T ss_dssp             CSCCCSEEEEES-----CCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEE
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeE
Confidence            344678899999     99999999999999999976   6777778999999999999999999999999999999999


Q ss_pred             EEEEEccCC
Q psy3345          88 IKVEKCSNL   96 (787)
Q Consensus        88 i~v~~~~~~   96 (787)
                      |.|.++++.
T Consensus        83 l~v~~a~~~   91 (101)
T 2fc9_A           83 IRLELQGPR   91 (101)
T ss_dssp             EEEEECSSC
T ss_pred             EEEEEcCCC
Confidence            999999873

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.1e-15  Score=133.36  Aligned_cols=82  Identities=18%  Similarity=0.393  Sum_probs=76.3

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||.|||..+|+++|+++|+.||.|..|+|+.+. .+|.++|||||+|.+.++|.+|+ .|| +..+.|+.|.|+|
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A~-~l~-g~~~~g~~l~V~~  100 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR-NSRRSKGIAYVEFCEIQSVPLAI-GLT-GQRLLGVPIIVQA  100 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC-CSSSCCCCEEEEESCGGGHHHHH-HHT-TEEETTEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecC-CCCccCcEEEEEeCcHHHHHHHH-HcC-CCEeCCeEEEEEe
Confidence            45899999999999999999999999999999999885 57899999999999999999999 997 7999999999999


Q ss_pred             ccccc
Q psy3345         764 AEEAD  768 (787)
Q Consensus       764 A~~~~  768 (787)
                      |.++.
T Consensus       101 a~~~~  105 (114)
T 2cq4_A          101 SQAEK  105 (114)
T ss_dssp             HHHHH
T ss_pred             cCCCc
Confidence            98654

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=5.1e-15  Score=129.65  Aligned_cols=80  Identities=19%  Similarity=0.177  Sum_probs=74.3

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      ..+...|+|.|     ||+++|+++|+++|+.||.|.+|.|+.  +++++|||||.|.+.++|++||+.||+..|.|+.|
T Consensus        19 ~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~v~~~~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           19 GNNDCRIYVGN-----LPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             CCCSSEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEE--CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34567899999     999999999999999999999999965  46789999999999999999999999999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.++++
T Consensus        92 ~V~~a~~   98 (109)
T 1x4a_A           92 RVEFPRS   98 (109)
T ss_dssp             EEECCCC
T ss_pred             EEEEccc
Confidence            9999987

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.59  E-value=3.7e-15  Score=132.02  Aligned_cols=82  Identities=21%  Similarity=0.243  Sum_probs=76.7

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .|+.++..|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.+  |+++|||||.|.+.++|.+|++.||+..|+|+
T Consensus         3 ~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   75 (115)
T 3lqv_A            3 LPPEVNRILYIRN-----LPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNR   75 (115)
T ss_dssp             CCTTCCSEEEEES-----CCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSC
T ss_pred             CCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            3566788999999     9999999999999999999999999865  67799999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.++.+
T Consensus        76 ~l~v~~a~~   84 (115)
T 3lqv_A           76 YLVVLYYNA   84 (115)
T ss_dssp             BCEEEECCH
T ss_pred             EEEEEEecC
Confidence            999999986

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.58  E-value=4.2e-15  Score=129.18  Aligned_cols=79  Identities=18%  Similarity=0.306  Sum_probs=71.8

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcC-CeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G-~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ...++|||+|||+.+|+++|+++|++|| .|..++|+.+     .++|||||+|.+.++|.+|+..|| +..+.|+.|.|
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~-----~~rGfaFV~F~~~e~A~~Ai~~ln-g~~l~Gr~i~V   99 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR-----DFDGTGALEFPSEEILVEALERLN-NIEFRGSVITV   99 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC-----SSSCCEEEEESSHHHHHHHHHHTT-TEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC-----CCCCEEEEEECCHHHHHHHHHHcC-CCEECCeEEEE
Confidence            3568999999999999999999999999 9999998643     378999999999999999999997 79999999999


Q ss_pred             EEcccc
Q psy3345         762 EWAEEA  767 (787)
Q Consensus       762 ~~A~~~  767 (787)
                      ++|...
T Consensus       100 ~~a~~~  105 (111)
T 2jvr_A          100 ERDDNP  105 (111)
T ss_dssp             EESCC-
T ss_pred             EECCCC
Confidence            999743

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=7.8e-15  Score=123.52  Aligned_cols=78  Identities=17%  Similarity=0.302  Sum_probs=73.5

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      +++..+..+|+|.|     ||+++|+++|+++|+.||.|.+|.|+       +|||||.|.+.++|.+|++.||+..|.|
T Consensus         2 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g   69 (90)
T 2dnq_A            2 SSGSSGMVKLFIGN-----LPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHG   69 (90)
T ss_dssp             CSCSSCCEEEEEES-----CCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCCCCeEEEEeC-----CCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCC
Confidence            45666788999999     99999999999999999999999998       5899999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus        70 ~~l~v~~a~~   79 (90)
T 2dnq_A           70 VNINVEASKN   79 (90)
T ss_dssp             CBCEEECSSC
T ss_pred             cEEEEEECCC
Confidence            9999999987

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=3.9e-15  Score=129.02  Aligned_cols=83  Identities=20%  Similarity=0.352  Sum_probs=76.4

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeE-EEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~-v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ....++|||+|||+.+|+++|+++|+.||.|.. |+|+.+  .+|+++|||||+|.++++|.+||.. + +..+.||.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~--~~g~~~G~afV~F~~~~~a~~A~~~-~-~~~~~gr~i~   87 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD--FQGRSTGEAFVQFASQEIAEKALKK-H-KERIGHRYIE   87 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC--SSSCBCSEEEEEESSHHHHHHHHTT-T-TCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC--CCCCcceEEEEEECCHHHHHHHHHh-C-cchhCCcEEE
Confidence            356789999999999999999999999999987 889888  5899999999999999999999997 5 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |.+|.+.+
T Consensus        88 v~~~~~~~   95 (104)
T 1wg5_A           88 IFKSSRAE   95 (104)
T ss_dssp             EEEECTTT
T ss_pred             EEECCHHH
Confidence            99998654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=3.5e-15  Score=133.22  Aligned_cols=81  Identities=15%  Similarity=0.229  Sum_probs=73.9

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHH----HHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      +..|+..|+|.|     ||+.+++++|+    ++|+.||.|.+|.+.  ++|+++|||||.|.+.++|..|++.|||..|
T Consensus        25 ~~~p~~~LfV~n-----L~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l   97 (127)
T 2a3j_A           25 HTEPSQVVLITN-----INPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPF   97 (127)
T ss_dssp             CCSCCSEEEEES-----CCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCC
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEe
Confidence            345677899999     99999999976    699999999998775  4689999999999999999999999999999


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      .||.|.|.+|++
T Consensus        98 ~gr~l~V~~a~~  109 (127)
T 2a3j_A           98 QGNPLVITFSET  109 (127)
T ss_dssp             TTSCCEEEECCC
T ss_pred             CCCEEEEEEccC
Confidence            999999999986

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.9e-15  Score=123.35  Aligned_cols=77  Identities=21%  Similarity=0.440  Sum_probs=71.2

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|++||.|.+++++++       +|||||+|.+.++|.+|+..|+++..+.|++|.|
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            456789999999999999999999999999999999875       7999999999999999999983479999999999


Q ss_pred             EEcc
Q psy3345         762 EWAE  765 (787)
Q Consensus       762 ~~A~  765 (787)
                      +||+
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.58  E-value=7.3e-16  Score=129.93  Aligned_cols=81  Identities=30%  Similarity=0.472  Sum_probs=72.5

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      ++|||+|||..+|+++|+++|++||.|.+++++++. .+|.++|||||+|.+.+ |.+|+..|| +..+.|++|.|+||.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~-a~~a~~~l~-g~~~~g~~l~V~~a~   78 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVEMQEES-VSEAIAKLD-NTDFMGRTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCS-SSCCCCEEEEEEECTTH-HHHHHHTSC-SSCCSSSSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcC-CCCCcceEEEEEECCHH-HHHHHHHhC-CCEECCeEEEEEEcC
Confidence            579999999999999999999999999999999885 57999999999999999 999999997 799999999999998


Q ss_pred             cccc
Q psy3345         766 EADN  769 (787)
Q Consensus       766 ~~~~  769 (787)
                      +...
T Consensus        79 ~~~~   82 (90)
T 2ki2_A           79 PKKS   82 (90)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            7654

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.58  E-value=7.2e-16  Score=129.96  Aligned_cols=76  Identities=28%  Similarity=0.455  Sum_probs=71.2

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      +|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.+ |.+|+..||+..++|+.|.|.+
T Consensus         3 ~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~   76 (90)
T 2ki2_A            3 NIYVGN-----LVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTE   76 (90)
T ss_dssp             EEEEEE-----ECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEE
T ss_pred             EEEECC-----CCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEE
Confidence            578888     99999999999999999999999999987 5999999999999999 9999999999999999999999


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      |.+
T Consensus        77 a~~   79 (90)
T 2ki2_A           77 ANP   79 (90)
T ss_dssp             C--
T ss_pred             cCC
Confidence            987

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=2e-15  Score=133.39  Aligned_cols=78  Identities=14%  Similarity=0.249  Sum_probs=74.2

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      +..|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|| .||+..|+|+.|.|
T Consensus        25 ~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   98 (114)
T 2cq4_A           25 ARTVFCMQ-----LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIV   98 (114)
T ss_dssp             HTEEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEE
T ss_pred             CCEEEEeC-----CCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEE
Confidence            35799999     99999999999999999999999999988 5999999999999999999999 89999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|++
T Consensus        99 ~~a~~  103 (114)
T 2cq4_A           99 QASQA  103 (114)
T ss_dssp             EEHHH
T ss_pred             EecCC
Confidence            99986

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.58  E-value=2.8e-15  Score=132.98  Aligned_cols=83  Identities=17%  Similarity=0.242  Sum_probs=76.7

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCC---eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGE---LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR  758 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~---I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~  758 (787)
                      ....++|||+|||+.+|+++|+++|+.||.   |.+|+|+.+.  .|+++|||||+|.+.++|.+||. ++ +..+.||.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~--~g~~~G~afV~F~~~~~a~~Al~-~~-g~~~~gr~   89 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR--EGRQSGEAFVELESEDDVKLALK-KD-RESMGHRY   89 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS--SSCEEEEEEEEBSSHHHHHHHGG-GT-TEEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC--CCCCCeEEEEEECCHHHHHHHHh-cC-CCeECCeE
Confidence            456789999999999999999999999999   8999999985  59999999999999999999999 86 79999999


Q ss_pred             EEEEEccccc
Q psy3345         759 LVLEWAEEAD  768 (787)
Q Consensus       759 l~v~~A~~~~  768 (787)
                      |.|.+|.+++
T Consensus        90 i~V~~a~~~~   99 (118)
T 2db1_A           90 IEVFKSHRTE   99 (118)
T ss_dssp             EEEEEECHHH
T ss_pred             EEEEECCHHH
Confidence            9999998655

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=6.6e-15  Score=125.91  Aligned_cols=80  Identities=16%  Similarity=0.324  Sum_probs=73.3

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec--Cce
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY--GRR  758 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~--Gr~  758 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|.+|+++++       +|||||+|.+.++|.+|+..|| +..+.  |++
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-------~g~afV~f~~~~~A~~A~~~l~-g~~~~~~g~~   84 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-------DSFAYIQYESLDAAQAACAKMR-GFPLGGPDRR   84 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-------SCCEEEEESSHHHHHHHHHHHT-TCBCSSSSCB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-------CCEEEEEECCHHHHHHHHHHHC-CCEeCCCCcE
Confidence            3456789999999999999999999999999999999764       6899999999999999999997 69999  999


Q ss_pred             EEEEEccccc
Q psy3345         759 LVLEWAEEAD  768 (787)
Q Consensus       759 l~v~~A~~~~  768 (787)
                      |.|+||.++.
T Consensus        85 l~V~~a~~~~   94 (97)
T 1why_A           85 LRVDFAKSGP   94 (97)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEECCCCC
Confidence            9999999764

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.58  E-value=1.8e-15  Score=136.68  Aligned_cols=83  Identities=17%  Similarity=0.223  Sum_probs=76.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCC---eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGE---LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR  758 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~---I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~  758 (787)
                      ....++|||+|||+.+|+++|+++|+.||.   |.+|+|+++.  .|+++|||||+|.+.++|.+||. +| +..+.||.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~--~g~srG~aFV~F~~~e~a~~Al~-~~-g~~l~gr~  116 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR--EGRQSGEAFVELGSEDDVKMALK-KD-RESMGHRY  116 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECS--SSCEEEEEEEECSSHHHHHHHHT-TT-EEESSSSE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECC--CCCCCeEEEEEECCHHHHHHHHh-cC-CCEECCEE
Confidence            446789999999999999999999999999   8999999985  49999999999999999999999 86 79999999


Q ss_pred             EEEEEccccc
Q psy3345         759 LVLEWAEEAD  768 (787)
Q Consensus       759 l~v~~A~~~~  768 (787)
                      |.|.+|.+++
T Consensus       117 i~V~~a~~~e  126 (136)
T 2hgl_A          117 IEVFKSHRTE  126 (136)
T ss_dssp             EEEEECCHHH
T ss_pred             EEEEECChHH
Confidence            9999998655

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=6.1e-15  Score=130.35  Aligned_cols=84  Identities=19%  Similarity=0.446  Sum_probs=77.5

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee-------
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL-------  754 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~-------  754 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|.+++|+++.  +|.++|||||+|.+.++|.+|+..|| +..+       
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~--~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~~~~~~~   98 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS--SGTSRGVGFARMESTEKCEAVIGHFN-GKFIKTPPGVS   98 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS--SSCEEEEEEEEESCHHHHHHHHHHHB-TCCCCCCTTSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC--CCCcceEEEEEECCHHHHHHHHHHhC-CCEEcCCcccc
Confidence            4567899999999999999999999999999999999984  89999999999999999999999997 6888       


Q ss_pred             -cCceEEEEEccccc
Q psy3345         755 -YGRRLVLEWAEEAD  768 (787)
Q Consensus       755 -~Gr~l~v~~A~~~~  768 (787)
                       .|++|.|.||.|..
T Consensus        99 ~~~~~l~v~~a~p~~  113 (114)
T 1x5o_A           99 APTEPLLCKFSGPSS  113 (114)
T ss_dssp             CCSSCBEEEECCCSC
T ss_pred             CCCCceeEEccCCCC
Confidence             68899999998753

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=6.3e-15  Score=128.97  Aligned_cols=77  Identities=18%  Similarity=0.268  Sum_probs=71.1

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc--CccCCc
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN--TYVFSS   86 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~--~~~~~~   86 (787)
                      ..|+..|+|.|     ||+++||+||+++|+.||.|.+|.|+.+     +|||||.|.+.++|.+|++.|++  ..|.||
T Consensus        28 ~~ps~~LfVgN-----Lp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr   97 (119)
T 2ad9_A           28 GVPSRVIHIRK-----LPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   97 (119)
T ss_dssp             SSCCSEEEEES-----CCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTB
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCe
Confidence            34577899999     9999999999999999999999999875     79999999999999999999885  689999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|++
T Consensus        98 ~l~V~~a~~  106 (119)
T 2ad9_A           98 PIYIQFSNH  106 (119)
T ss_dssp             CCEEEECSS
T ss_pred             EEEEEEccC
Confidence            999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.58  E-value=2.1e-15  Score=137.17  Aligned_cols=84  Identities=21%  Similarity=0.386  Sum_probs=78.5

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .+..+...|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|++||+.||+..|+|
T Consensus        42 ~~~~~~~~l~V~n-----Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g  116 (135)
T 2lea_A           42 PDVEGMTSLKVDN-----LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG  116 (135)
T ss_dssp             SSGGGCCCEEEEC-----CCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSS
T ss_pred             CCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3444566799999     99999999999999999999999999987 79999999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus       117 ~~l~V~~a~~  126 (135)
T 2lea_A          117 RELRVQMARY  126 (135)
T ss_dssp             SCCEEEECCC
T ss_pred             EEEEEEECCC
Confidence            9999999987

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=6e-15  Score=127.24  Aligned_cols=82  Identities=21%  Similarity=0.460  Sum_probs=74.6

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|++||.|   +++.+  .+|+++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~--~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~   84 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN--QNGKSKGYAFIEFASFEDAKEALNSCN-KREIEGRAIR   84 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC--SSSCBCSEEEEECSSHHHHHHHHHHTS-SEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC--CCCCEeeEEEEEECCHHHHHHHHHHhC-CCEeCCeEEE
Confidence            34578999999999999999999999999977   66666  478999999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.+..
T Consensus        85 v~~a~~~~   92 (101)
T 2fc9_A           85 LELQGPRG   92 (101)
T ss_dssp             EEECSSCC
T ss_pred             EEEcCCCC
Confidence            99998764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=1.2e-15  Score=127.02  Aligned_cols=81  Identities=28%  Similarity=0.429  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      .++++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.+++.+.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45779999999999999999999999999999999999889999999999999999999999999999999999988765


Q ss_pred             C
Q psy3345         414 K  414 (787)
Q Consensus       414 ~  414 (787)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.58  E-value=1.8e-15  Score=124.55  Aligned_cols=74  Identities=23%  Similarity=0.397  Sum_probs=68.2

Q ss_pred             CCEEEEecCCccC------cHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc-
Q psy3345         685 GSKILVRNIPFQA------KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR-  757 (787)
Q Consensus       685 ~~~l~V~nLp~~~------t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr-  757 (787)
                      +++|||+|||..+      |+++|+++|++||.|.+++|++   .+|+++|||||+|.+.++|.+|+..|| |..+.|+ 
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~---~~g~~~g~afV~f~~~~~A~~Ai~~ln-g~~~~g~~   76 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE---EDGKTKGYIFLEYASPAHAVDAVKNAD-GYKLDKQH   76 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC---BTTBCCCEEEEEESSHHHHHHHHTTSS-SCCCSSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC---CCCcEeEEEEEEECCHHHHHHHHHHhc-CcccCCce
Confidence            4689999999999      7899999999999999999984   389999999999999999999999997 7999999 


Q ss_pred             eEEEE
Q psy3345         758 RLVLE  762 (787)
Q Consensus       758 ~l~v~  762 (787)
                      +|+|+
T Consensus        77 ~l~V~   81 (81)
T 2krb_A           77 TFRVN   81 (81)
T ss_dssp             CCCCC
T ss_pred             eEEeC
Confidence            88763

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.58  E-value=4.4e-15  Score=136.71  Aligned_cols=82  Identities=26%  Similarity=0.440  Sum_probs=76.2

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ++..+..+|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+|++.||+..|+|
T Consensus        58 ~~~~~~~~l~v~n-----lp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  132 (140)
T 2ku7_A           58 GSATTKRVLYVGG-----LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG  132 (140)
T ss_dssp             SSCSSCCEEEEEC-----CCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETT
T ss_pred             CCCCCCcEEEEEe-----CCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3455678899999     99999999999999999999999999986 79999999999999999999999999999999


Q ss_pred             ceEEEEEc
Q psy3345          86 SRIKVEKC   93 (787)
Q Consensus        86 ~~i~v~~~   93 (787)
                      +.|.|.+|
T Consensus       133 ~~l~v~~A  140 (140)
T 2ku7_A          133 RTIRVNLA  140 (140)
T ss_dssp             EEEEEEC-
T ss_pred             EEEEEEeC
Confidence            99999875

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=8.4e-15  Score=129.45  Aligned_cols=82  Identities=11%  Similarity=0.246  Sum_probs=77.0

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc-----
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV-----   83 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~-----   83 (787)
                      ..+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.+++|+++|||||.|.+.++|.+|++.||+..|     
T Consensus        22 ~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~   96 (114)
T 1x5o_A           22 EQDPTNLYISN-----LPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   96 (114)
T ss_dssp             CCCTTEEEEES-----CCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcc
Confidence            45677899999     99999999999999999999999999999999999999999999999999999999999     


Q ss_pred             ---CCceEEEEEccC
Q psy3345          84 ---FSSRIKVEKCSN   95 (787)
Q Consensus        84 ---~~~~i~v~~~~~   95 (787)
                         .++.|.|.+|.+
T Consensus        97 ~~~~~~~l~v~~a~p  111 (114)
T 1x5o_A           97 VSAPTEPLLCKFSGP  111 (114)
T ss_dssp             SCCCSSCBEEEECCC
T ss_pred             ccCCCCceeEEccCC
Confidence               577899999986

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=4.2e-15  Score=131.85  Aligned_cols=83  Identities=23%  Similarity=0.393  Sum_probs=77.5

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      +.++|||.|||..+|+++|+++|+.||.|..|+|+.+. .+|.++|||||+|.+.++|.+||.. + +..+.|++|.|.|
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~Ai~~-~-~~~~~g~~l~V~~  102 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP-ASKRSRGFGFVTFSSMAEVDAAMAA-R-PHSIDGRVVEPKR  102 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCT-TTSSCCSEEEEECSSHHHHHHHHTS-C-SEEETTEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCcCceEEEEeCCHHHHHHHHHh-C-CcEECCEEEEEEE
Confidence            45899999999999999999999999999999999985 6799999999999999999999998 5 7999999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      |.++..
T Consensus       103 a~~~~~  108 (116)
T 1x4b_A          103 AVAREE  108 (116)
T ss_dssp             CSSCCC
T ss_pred             CCCCcc
Confidence            997764

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.57  E-value=8e-15  Score=134.97  Aligned_cols=82  Identities=24%  Similarity=0.482  Sum_probs=76.1

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||+|||..+|+++|+++|++||.|.+++|+++. .+|+++|||||+|.+.++|.+|+..|| +..+.|++|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~  136 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMN-ESELFGRTIR  136 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCT-TTCCCCSEEEEEESCHHHHHHHHHHST-EEEETTEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecC-CCCCcCcEEEEEECCHHHHHHHHHHhC-CCEECCEEEE
Confidence            34578999999999999999999999999999999999885 689999999999999999999999997 7999999999


Q ss_pred             EEEc
Q psy3345         761 LEWA  764 (787)
Q Consensus       761 v~~A  764 (787)
                      |+||
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            9997

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=8.8e-15  Score=124.98  Aligned_cols=77  Identities=16%  Similarity=0.230  Sum_probs=70.7

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc--cCccCCc
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN--NTYVFSS   86 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~--~~~~~~~   86 (787)
                      ..|+..|+|+|     ||+.+|++||+++|+.||.|.+|.|+.+     +|||||.|.+.++|.+|++.|+  +..+.||
T Consensus        12 ~~p~~~l~V~n-----Lp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   81 (101)
T 2cq1_A           12 GAPSRVLHIRK-----LPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   81 (101)
T ss_dssp             SSCCSEEEEES-----CCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCc
Confidence            34678899999     9999999999999999999999988864     8999999999999999999875  5689999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|++
T Consensus        82 ~l~V~~a~~   90 (101)
T 2cq1_A           82 PIYIQYSNH   90 (101)
T ss_dssp             ECEEEECSC
T ss_pred             EEEEEEcCc
Confidence            999999986

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.57  E-value=9.9e-15  Score=136.87  Aligned_cols=86  Identities=23%  Similarity=0.412  Sum_probs=79.5

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|.+|+|+.+. .++.++|||||+|.+.++|.+||..|| +..+.|+.|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~V  113 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKKTACGFCFVEYYSRADAENAMRYIN-GTRLDDRIIRT  113 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHTT-TSEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCccceEEEEEECCHHHHHHHHHHhC-CCEECCeEEEE
Confidence            3467999999999999999999999999999999999885 578999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.+...
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99986553

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=4.7e-15  Score=131.50  Aligned_cols=80  Identities=15%  Similarity=0.255  Sum_probs=75.4

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      +..+|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+||+. |+..|+|+.|.
T Consensus        26 ~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~   99 (116)
T 1x4b_A           26 QFRKLFIGG-----LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVE   99 (116)
T ss_dssp             HHTEEEEEC-----CTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEE
Confidence            346799999     99999999999999999999999999987 699999999999999999999999 99999999999


Q ss_pred             EEEccCC
Q psy3345          90 VEKCSNL   96 (787)
Q Consensus        90 v~~~~~~   96 (787)
                      |.+|.+.
T Consensus       100 V~~a~~~  106 (116)
T 1x4b_A          100 PKRAVAR  106 (116)
T ss_dssp             EECCSSC
T ss_pred             EEECCCC
Confidence            9999874

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.57  E-value=3.1e-15  Score=127.50  Aligned_cols=80  Identities=24%  Similarity=0.273  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      ..++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            45799999999999999999999999999999898888889999999999999999999999999999999999999875

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.57  E-value=1.9e-15  Score=124.52  Aligned_cols=73  Identities=15%  Similarity=0.195  Sum_probs=67.7

Q ss_pred             cceEEEecCcccCCCccC------CHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345          12 RNHISLLDLDEVEFIYKI------TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ++.|+|.|     ||+.+      |+++|+++|+.||.|.+|.|+ ..+|+++|||||.|.+.++|.+|++.|||..|+|
T Consensus         1 ~~~l~V~n-----Lp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g   74 (81)
T 2krb_A            1 DSVIVVDN-----VPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   74 (81)
T ss_dssp             CCEEEEES-----CCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSS
T ss_pred             CCEEEEeC-----CCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCC
Confidence            35788888     99999      789999999999999999988 4589999999999999999999999999999999


Q ss_pred             c-eEEE
Q psy3345          86 S-RIKV   90 (787)
Q Consensus        86 ~-~i~v   90 (787)
                      | .|.|
T Consensus        75 ~~~l~V   80 (81)
T 2krb_A           75 QHTFRV   80 (81)
T ss_dssp             SSCCCC
T ss_pred             ceeEEe
Confidence            9 8876

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.57  E-value=1.4e-15  Score=137.99  Aligned_cols=80  Identities=18%  Similarity=0.172  Sum_probs=75.9

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEE--EEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccC----c
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD--VQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNT----Y   82 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~--~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~----~   82 (787)
                      .+..+|+|.|     ||+++|+++|+++|+.||.|..  |+|++++ +|+++|||||.|.+. +|.+|+..||+.    .
T Consensus        21 ~~~~~lfV~n-----L~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           21 NANDTIILRN-----LNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CCCCEEEECS-----CCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            4567899999     9999999999999999999966  9999999 899999999999999 999999999999    9


Q ss_pred             cCCceEEEEEccC
Q psy3345          83 VFSSRIKVEKCSN   95 (787)
Q Consensus        83 ~~~~~i~v~~~~~   95 (787)
                      |+||.|.|.+|++
T Consensus        95 ~~gr~l~V~~a~~  107 (131)
T 2m2b_A           95 IDGKTINVEFAKG  107 (131)
T ss_dssp             GGGCCCCCEECCC
T ss_pred             CCCEEEEEEECCC
Confidence            9999999999987

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.57  E-value=4.9e-15  Score=133.18  Aligned_cols=78  Identities=19%  Similarity=0.339  Sum_probs=74.4

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ...|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|.+|+ .||+..|+|+.|.|
T Consensus        36 ~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V  109 (124)
T 2jwn_A           36 KRSVYVGN-----VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKV  109 (124)
T ss_dssp             HTEEEEEE-----ECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEE
T ss_pred             CCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEE
Confidence            45799999     99999999999999999999999999986 8999999999999999999999 79999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .++++
T Consensus       110 ~~a~~  114 (124)
T 2jwn_A          110 LPKRT  114 (124)
T ss_dssp             EESSC
T ss_pred             EECCC
Confidence            99986

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.56  E-value=2e-15  Score=131.54  Aligned_cols=83  Identities=13%  Similarity=0.173  Sum_probs=76.7

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCC---eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGE---LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR  758 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~---I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~  758 (787)
                      ....++|||+|||+.+|+++|+++|+.||.   |.+|+|+.+.  .|+++|||||+|.+.++|.+||. ++ +..+.||.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~--~g~~~G~afV~F~~~~~a~~Al~-~~-~~~~~gr~   83 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR--DGKRRGDALIEMESEQDVQKALE-KH-RMYMGQRY   83 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCT--TSTTCSEEEEEBSSHHHHHHHHT-TT-TCCSSSSC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECC--CCCEeeEEEEEECCHHHHHHHHH-hC-cceeCCeE
Confidence            456789999999999999999999999998   8999999985  49999999999999999999999 86 79999999


Q ss_pred             EEEEEccccc
Q psy3345         759 LVLEWAEEAD  768 (787)
Q Consensus       759 l~v~~A~~~~  768 (787)
                      |.|.+|.+++
T Consensus        84 i~V~~a~~~~   93 (107)
T 2lmi_A           84 VEVYEINNED   93 (107)
T ss_dssp             CCCEECCHHH
T ss_pred             EEEEECCHHH
Confidence            9999998765

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.56  E-value=1.2e-14  Score=136.28  Aligned_cols=81  Identities=17%  Similarity=0.286  Sum_probs=77.5

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .++..|+|.|     ||+.+|+++|+++|+.||.|..|+|+.++ +|+++|||||.|.+.++|.+||+.||+..|+|+.|
T Consensus        37 ~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  111 (156)
T 1h2v_Z           37 KKSCTLYVGN-----LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII  111 (156)
T ss_dssp             TTCCEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEEC
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            4677899999     99999999999999999999999999988 69999999999999999999999999999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.+|++
T Consensus       112 ~V~~a~~  118 (156)
T 1h2v_Z          112 RTDWDAG  118 (156)
T ss_dssp             EEEEESC
T ss_pred             EEEECCC
Confidence            9999987

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=7e-15  Score=126.27  Aligned_cols=80  Identities=28%  Similarity=0.458  Sum_probs=73.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|++||.|..|+++++       +|||||+|.+.++|.+|+..|+ +..+.|++|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-------kg~afV~f~~~~~a~~a~~~l~-g~~~~g~~l~v   83 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-------KGFGFIRLETRTLAEIAKVELD-NMPLRGKQLRV   83 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-------TTEEEEECSSSHHHHHHHHHHT-TCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------CCEEEEEECCHHHHHHHHHHhC-CCEeCCceEEE
Confidence            456789999999999999999999999999999999865       7899999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.+...
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpj_A           84 RFACHSAS   91 (99)
T ss_dssp             EESSCCSC
T ss_pred             EEcCCCCC
Confidence            99987654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.2e-14  Score=122.37  Aligned_cols=78  Identities=23%  Similarity=0.439  Sum_probs=72.1

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|++||.|.+++++         +|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---------~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v   74 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---------KNYGFVHIEDKTAAEDAIRNLH-HYKLHGVNINV   74 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---------TTEEEEEESSHHHHHHHHHHHT-TCBCSSCBCEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---------CCEEEEEECCHHHHHHHHHHhc-CCccCCcEEEE
Confidence            4567899999999999999999999999999999996         4799999999999999999997 69999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus        75 ~~a~~~~~   82 (90)
T 2dnq_A           75 EASKNKSK   82 (90)
T ss_dssp             ECSSCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.2e-14  Score=122.33  Aligned_cols=78  Identities=27%  Similarity=0.369  Sum_probs=73.0

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .++..+..+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.       +||||.|.+.++|++|++.||+..|+|
T Consensus         3 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g   70 (90)
T 2dnp_A            3 SGSSGNTWKIFVGN-----VSAACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKG   70 (90)
T ss_dssp             CCSSCCSCCEEEES-----CCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            45667788999999     999999999999999999999999973       499999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus        71 ~~l~v~~a~~   80 (90)
T 2dnp_A           71 KRINVELSTK   80 (90)
T ss_dssp             EECEEEESCC
T ss_pred             cEEEEEECCC
Confidence            9999999987

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.56  E-value=5e-15  Score=128.22  Aligned_cols=79  Identities=24%  Similarity=0.429  Sum_probs=72.0

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||..+|+++|+++|+.||.|..|+|++         |||||+|.+.++|.+|+..|| +..+.|+.|.|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~---------~~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v   77 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---------DYAFIHFDERDGAVKAMEEMN-GKDLEGENIEI   77 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS---------SCEEEEESSHHHHHHHHHHHT-TEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC---------CEEEEEeCCHHHHHHHHHHHC-CCccCCCEEEE
Confidence            34678999999999999999999999999999999863         589999999999999999997 79999999999


Q ss_pred             EEccccccH
Q psy3345         762 EWAEEADNV  770 (787)
Q Consensus       762 ~~A~~~~~~  770 (787)
                      +||.+....
T Consensus        78 ~~a~~~~~~   86 (103)
T 2dgu_A           78 VFAKPPDQK   86 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEcCCCccc
Confidence            999976653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.56  E-value=7.4e-15  Score=131.98  Aligned_cols=81  Identities=20%  Similarity=0.368  Sum_probs=75.5

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||..+|+++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|+ .|| +..+.|+.|.|+|
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A~-~l~-g~~~~g~~l~V~~  111 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDK-FSGHPKGYAYIEFAERNSVDAAV-AMD-ETVFRGRTIKVLP  111 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEEC-TTSSCEEEEEEEESSHHHHHHHH-TTT-TCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCCcccEEEEEECCHHHHHHHH-hcC-CCeECCeEEEEEE
Confidence            45899999999999999999999999999999999885 58999999999999999999999 786 7999999999999


Q ss_pred             cccc
Q psy3345         764 AEEA  767 (787)
Q Consensus       764 A~~~  767 (787)
                      |++.
T Consensus       112 a~~~  115 (124)
T 2jwn_A          112 KRTN  115 (124)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9854

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=1.6e-14  Score=126.03  Aligned_cols=79  Identities=15%  Similarity=0.363  Sum_probs=73.2

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC-----
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG-----  756 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G-----  756 (787)
                      ....++|||.|||+.+|+++|+++|+.||.|..|+|+.+        |||||+|.+.++|.+||..|| +..+.|     
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--------g~afV~f~~~~~a~~Ai~~l~-g~~~~g~~~~~   82 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVEFVRKEDMTYAVRKLD-NTKFRSHEGET   82 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--------TEEEEEESSHHHHHHHHHHSS-SEEEECTTSCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--------CEEEEEECCHHHHHHHHHHHC-cCCccCCcCcc
Confidence            356799999999999999999999999999999999775        899999999999999999997 799999     


Q ss_pred             ceEEEEEcccccc
Q psy3345         757 RRLVLEWAEEADN  769 (787)
Q Consensus       757 r~l~v~~A~~~~~  769 (787)
                      +.|.|+||.++..
T Consensus        83 ~~i~V~~a~~~~~   95 (108)
T 1x4c_A           83 AYIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEEESSCCSC
T ss_pred             eEEEEEeCCCCCC
Confidence            9999999997653

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=1.2e-14  Score=124.34  Aligned_cols=80  Identities=20%  Similarity=0.260  Sum_probs=74.1

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccC-
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF-   84 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~-   84 (787)
                      .+...++.+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+     +|||||.|.+.++|++|++.||+..|. 
T Consensus        11 ~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~   80 (97)
T 1why_A           11 YGKANPTTRLWVGG-----LGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGG   80 (97)
T ss_dssp             CCCCCCCSCEEEEC-----CCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            34556778999999     9999999999999999999999998754     789999999999999999999999999 


Q ss_pred             -CceEEEEEccC
Q psy3345          85 -SSRIKVEKCSN   95 (787)
Q Consensus        85 -~~~i~v~~~~~   95 (787)
                       |+.|.|.+|++
T Consensus        81 ~g~~l~V~~a~~   92 (97)
T 1why_A           81 PDRRLRVDFAKS   92 (97)
T ss_dssp             SSCBCEEEECCC
T ss_pred             CCcEEEEEECCC
Confidence             99999999987

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.56  E-value=6.2e-15  Score=127.19  Aligned_cols=76  Identities=30%  Similarity=0.494  Sum_probs=71.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      ++|||+|||+++|+++|+++|++||.|..|.++.+     ++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999876     7789999999999999999999999999999999999876


Q ss_pred             C
Q psy3345         417 E  417 (787)
Q Consensus       417 ~  417 (787)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.56  E-value=1e-15  Score=138.78  Aligned_cols=126  Identities=19%  Similarity=0.206  Sum_probs=75.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHH
Q psy3345         627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELF  706 (787)
Q Consensus       627 ~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F  706 (787)
                      +|+||.+|.-++.+..++..+... .+|...--..            ............++|||+|||+.+|+++|+++|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~------------g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F   67 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGS------------GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFF   67 (139)
T ss_dssp             ---------------------------------------------------------CCCCEECCSCCTTCCHHHHHHHH
T ss_pred             CCcccccccCccccchhcccchhc-cCCCCCCCCC------------CCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            367888888887777776655322 2222110000            000111233467899999999999999999999


Q ss_pred             HhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccccH
Q psy3345         707 KAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNV  770 (787)
Q Consensus       707 ~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~  770 (787)
                      +.|| |.+|+|+++.  +|+++|||||+|.+.++|.+|| .+| +..+.||.|.|.+|.+.+..
T Consensus        68 ~~~G-i~~v~i~~d~--~g~srGfaFV~F~~~e~A~~Al-~~~-g~~l~gR~i~V~~a~~~~~~  126 (139)
T 2hgn_A           68 SPLN-PVRVHIEIGP--DGRVTGEADVEFATHEEAVAAM-SKD-RANMQHRYIELFLNSTTGAS  126 (139)
T ss_dssp             CSCC-CSEEECCCSS--SSCSSCCCEEECSHHHHHHHHT-TCC-SCSSSSCCCCCEECCCSCC-
T ss_pred             HhcC-CeEEEEEECC--CCCCceEEEEEeCCHHHHHHHH-hhC-CCEECCEEEEEEECCCCCCC
Confidence            9999 7799999995  5999999999999999999999 675 79999999999999987753

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=6.4e-15  Score=127.79  Aligned_cols=79  Identities=23%  Similarity=0.380  Sum_probs=72.8

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||+.+|++||+++|+.| .|.+|+|+.+.  .|+++|||||+|.+.++|.+|| .+| +..+.||.|.|..
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~--~g~~~G~afV~F~~~~~a~~Al-~~~-~~~~~gr~i~V~~   89 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH--VGRNNGNGLVKFLSPQDTFEAL-KRN-RMLMIQRYVEVSP   89 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT--TCCCCSEEEEECSSHHHHHHHH-HTT-TEEETTEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC--CCCCCeEEEEEECCHHHHHHHH-hcC-CCeECCeEEEEEE
Confidence            34789999999999999999999999 79999999984  5999999999999999999999 676 7999999999999


Q ss_pred             cccc
Q psy3345         764 AEEA  767 (787)
Q Consensus       764 A~~~  767 (787)
                      |.++
T Consensus        90 a~~~   93 (109)
T 2dnn_A           90 ATER   93 (109)
T ss_dssp             CCHH
T ss_pred             CCcc
Confidence            9764

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=6.2e-15  Score=127.46  Aligned_cols=78  Identities=13%  Similarity=0.167  Sum_probs=70.5

Q ss_pred             CCcccceEEE--ecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc--
Q psy3345           8 PVVPRNHISL--LDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV--   83 (787)
Q Consensus         8 ~~~~~~~~~~--~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~--   83 (787)
                      ...|+.+|+|  .|     ||+++|+++|+++|+.||.|.+|.|+.     .+|||||.|.+.++|++|++.|||..+  
T Consensus        21 ~~~pt~~L~V~Ng~-----L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~   90 (114)
T 2cq2_A           21 VSYATQSLVVANGG-----LGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVD   90 (114)
T ss_dssp             CSSCCSEEEEETCT-----GGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCCCCEEEEECCC-----CCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEEcc
Confidence            3446778999  66     999999999999999999999998864     279999999999999999999999988  


Q ss_pred             ---CCceEEEEEccC
Q psy3345          84 ---FSSRIKVEKCSN   95 (787)
Q Consensus        84 ---~~~~i~v~~~~~   95 (787)
                         +|+.|.|.++..
T Consensus        91 ~lg~g~~l~v~~a~~  105 (114)
T 2cq2_A           91 DLGQKITLYLNFVEK  105 (114)
T ss_dssp             TTSCEEECEEEEESC
T ss_pred             ccCCCcEEEEEeccc
Confidence               799999999986

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=3.1e-15  Score=122.00  Aligned_cols=76  Identities=20%  Similarity=0.410  Sum_probs=72.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ++|||+|||+++|+++|+++|++||+|..+.++.++.+|.++|||||+|.+.++|.+|++.++ ..+.|+.|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999998889999999999999999999999888 9999999999876

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=9.4e-15  Score=125.67  Aligned_cols=77  Identities=14%  Similarity=0.241  Sum_probs=70.5

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccC--ccCCc
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT--YVFSS   86 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~--~~~~~   86 (787)
                      ..|+..|+|+|     ||+.+||++|+++|+.||.|.+|.|+.+     +|||||.|.+.++|.+|++.||+.  .|+||
T Consensus        12 ~~p~~~l~V~n-----Lp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr   81 (104)
T 1wex_A           12 VSVSPVVHVRG-----LCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCSEEEEES-----CCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            34678899999     9999999999999999999999998864     799999999999999999998764  59999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|++
T Consensus        82 ~l~V~~a~~   90 (104)
T 1wex_A           82 QAFFNYSTS   90 (104)
T ss_dssp             BCEEEECSS
T ss_pred             EEEEEEccC
Confidence            999999986

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1.3e-14  Score=127.00  Aligned_cols=80  Identities=20%  Similarity=0.408  Sum_probs=74.3

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||+|||..+|+++|+++|+.||.|.+|+|+++       +|||||+|.+.++|.+|+..|+ +..+.|++|.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-------~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v   93 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-------KGYSFVRFSTHESAAHAIVSVN-GTTIEGHVVKC   93 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-------CCEEEEEECCHHHHHHHHHHcC-CCEECCcEEEE
Confidence            346789999999999999999999999999999999876       7899999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      .||+++..
T Consensus        94 ~~a~~~~~  101 (109)
T 1x4g_A           94 YWGKESPD  101 (109)
T ss_dssp             ECCCCCCS
T ss_pred             EecCCCCC
Confidence            99997664

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=7.3e-15  Score=128.74  Aligned_cols=75  Identities=33%  Similarity=0.503  Sum_probs=70.0

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||..+|+++|+++|++||.|.+|+|++       ++|||||+|.+.++|.+|+..|| +..+.|++|.|+|
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-------~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~V~~   80 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-------GGITAIVEFLEPLEARKAFRHLA-YSKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-------SSSCEEEEESCHHHHHHHHHHHT-TCBSSSSBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-------CCCEEEEEeCCHHHHHHHHHHhC-CCEECCeEEEEEE
Confidence            467999999999999999999999999999999875       37899999999999999999997 7999999999999


Q ss_pred             ccc
Q psy3345         764 AEE  766 (787)
Q Consensus       764 A~~  766 (787)
                      |..
T Consensus        81 a~~   83 (111)
T 1whx_A           81 API   83 (111)
T ss_dssp             EET
T ss_pred             CCC
Confidence            974

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.1e-14  Score=124.55  Aligned_cols=81  Identities=20%  Similarity=0.314  Sum_probs=72.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      .....++|||.|||..+|+++|+++|+.||.|. ++++.+     .++|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~-----~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   87 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ-----GPRRRAFLHYPDSAAAQQAVSCLQ-GLRLGTDTLR   87 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE-----TTTTEEEEECSSHHHHHHHHHHHT-TCCSSSSCCE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC-----CCCcEEEEEECCHHHHHHHHHHhC-CCEECCcEEE
Confidence            345678999999999999999999999999996 666543     578999999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.++.
T Consensus        88 V~~a~~~~   95 (97)
T 2e5j_A           88 VALARQQR   95 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99998764

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=1.5e-14  Score=126.31  Aligned_cols=76  Identities=17%  Similarity=0.171  Sum_probs=71.8

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC---
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS---   85 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~---   85 (787)
                      ..+..+|+|.|     ||+++|++||+++|+.||.|.+|.|+.+      |||||+|.+.++|++||+.||+..|.|   
T Consensus        12 ~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~   80 (108)
T 1x4c_A           12 RRSENRVVVSG-----LPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   80 (108)
T ss_dssp             CSCCCEEEEES-----CCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTS
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcC
Confidence            34567899999     9999999999999999999999999886      899999999999999999999999999   


Q ss_pred             --ceEEEEEccC
Q psy3345          86 --SRIKVEKCSN   95 (787)
Q Consensus        86 --~~i~v~~~~~   95 (787)
                        +.|.|.+|.+
T Consensus        81 ~~~~i~V~~a~~   92 (108)
T 1x4c_A           81 ETAYIRVKVDGP   92 (108)
T ss_dssp             CEEEEEEEESSC
T ss_pred             cceEEEEEeCCC
Confidence              9999999987

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.1e-14  Score=124.15  Aligned_cols=83  Identities=16%  Similarity=0.295  Sum_probs=75.2

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      ..+..++.+|+|.|     ||+++|+++|+++|++|+   .|.++.++ +|+++|||||.|.+.++|.+||+.||+..|+
T Consensus         9 ~~~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   80 (102)
T 2fc8_A            9 NARSQPSKTLFVKG-----LSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID   80 (102)
T ss_dssp             SSSSCCCSSEEEEC-----CCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCCCEEEEeC-----CCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            34456778899999     999999999999999883   78888886 8999999999999999999999999999999


Q ss_pred             CceEEEEEccCC
Q psy3345          85 SSRIKVEKCSNL   96 (787)
Q Consensus        85 ~~~i~v~~~~~~   96 (787)
                      |+.|.|.+|++.
T Consensus        81 g~~l~V~~a~~~   92 (102)
T 2fc8_A           81 GNKVTLDWAKPK   92 (102)
T ss_dssp             TEECEEEECCCC
T ss_pred             CeEEEEEEecCC
Confidence            999999999973

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.55  E-value=2.2e-14  Score=122.38  Aligned_cols=78  Identities=18%  Similarity=0.513  Sum_probs=71.3

Q ss_pred             cCCCCCEEEEecCCc-cCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         681 AKQTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~-~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ...+.++|||+|||. .+|+++|+++|+.||.|.++++.         +|||||+|.+.++|.+|+..|| +..+.|++|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---------~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l   87 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---------NAFGFIQFDNPQSVRDAIEXES-QEMNFGKKL   87 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---------SSEEEEEESSHHHHHHHHHHHT-TSEETTEEC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---------CCEEEEEECCHHHHHHHHHHcC-CCEECCEEE
Confidence            345789999999998 99999999999999999999982         6899999999999999999997 699999999


Q ss_pred             EEEEccccc
Q psy3345         760 VLEWAEEAD  768 (787)
Q Consensus       760 ~v~~A~~~~  768 (787)
                      .|+||++..
T Consensus        88 ~V~~a~~~~   96 (97)
T 2xnq_A           88 ILEVSSSNA   96 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEecCCCC
Confidence            999998653

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.55  E-value=2.1e-15  Score=122.30  Aligned_cols=74  Identities=19%  Similarity=0.302  Sum_probs=69.0

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      +|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.++++|.+|++. ++..|+|+.|.|.+
T Consensus         1 ~l~v~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGG-----LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKV   74 (75)
T ss_dssp             CEEESC-----CCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEE
T ss_pred             CEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            367777     99999999999999999999999999987 699999999999999999999997 99999999999987


Q ss_pred             c
Q psy3345          93 C   93 (787)
Q Consensus        93 ~   93 (787)
                      |
T Consensus        75 a   75 (75)
T 1iqt_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=3e-15  Score=132.60  Aligned_cols=87  Identities=24%  Similarity=0.406  Sum_probs=74.2

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||.|||..+|+++|+++|+.||.|..+.+..+. .+|.++|||||+|.+.++|.+|+..|+ +..+.|++|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~g~~~g~afV~f~~~~~a~~Ai~~l~-g~~~~g~~l~   98 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-MTGRMRGQAFITFPNKEIAWQALHLVN-GYKLYGKILV   98 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE-ECSSSCSEEEEECSSHHHHHHHHHHST-TCBCSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEc-CCCccceEEEEEECCHHHHHHHHHHhC-CCEeCCcEEE
Confidence            34578999999999999999999999999999443332221 267899999999999999999999997 6999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.+...
T Consensus        99 v~~a~~~~~  107 (115)
T 2cpx_A           99 IEFGKNKKQ  107 (115)
T ss_dssp             EEECCCCSC
T ss_pred             EEEccCCCC
Confidence            999987653

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.2e-14  Score=121.26  Aligned_cols=78  Identities=23%  Similarity=0.356  Sum_probs=72.5

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ..+..+..+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.       +||||.|.+.++|.+|++.||+..|.|
T Consensus         4 ~~~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g   71 (92)
T 2dgt_A            4 GSSGKASTKLHVGN-----ISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQG   71 (92)
T ss_dssp             SCCCCSSEEEEEES-----CCSSCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            44556778899999     999999999999999999999999974       499999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus        72 ~~l~V~~a~~   81 (92)
T 2dgt_A           72 KRMHVQLSTS   81 (92)
T ss_dssp             EEEEEEESSC
T ss_pred             cEEEEEEccC
Confidence            9999999987

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=4.4e-15  Score=131.67  Aligned_cols=83  Identities=22%  Similarity=0.261  Sum_probs=75.2

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCe----eEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR  758 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I----~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~  758 (787)
                      ...++|||+|||+.+|++||+++|+.||.|    .+|+|+.+  .+|+++|||||+|.+.++|.+||.. + +..+.||.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d--~~gr~~G~aFV~F~~~~~A~~Al~~-~-~~~l~gR~   96 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY--PDGRPTGDAFVLFACEEYAQNALRK-H-KDLLGKRY   96 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC--TTSCEEEEEEECCSSHHHHHHHHTT-T-TEESSSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC--CCCCEeeEEEEEECCHHHHHHHHHh-C-CCeeCCeE
Confidence            457899999999999999999999999975    68999988  4899999999999999999999996 5 79999999


Q ss_pred             EEEEEcccccc
Q psy3345         759 LVLEWAEEADN  769 (787)
Q Consensus       759 l~v~~A~~~~~  769 (787)
                      |.|..|.+++-
T Consensus        97 i~V~~a~~~e~  107 (123)
T 2dha_A           97 IELFRSTAAEV  107 (123)
T ss_dssp             ECCEEECHHHH
T ss_pred             EEEEECCHHHH
Confidence            99999986553

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.55  E-value=8.7e-15  Score=126.24  Aligned_cols=77  Identities=25%  Similarity=0.415  Sum_probs=71.6

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||..+|+++|+++|+.||.|.++++++       ++|||||+|.+.++|.+|+..|| +..+.|++|+|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-------~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~V~   96 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-------EKGCCFIKYDTHEQAAVCIVALA-NFPFQGRNLRTG   96 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-------TTTEEEEECSSHHHHHHHHHHHT-TCEETTEECCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-------CCCEEEEEECCHHHHHHHHHHhC-CCeECCeEEEEE
Confidence            4578999999999999999999999999999999974       47999999999999999999997 799999999999


Q ss_pred             Ecccc
Q psy3345         763 WAEEA  767 (787)
Q Consensus       763 ~A~~~  767 (787)
                      ||+++
T Consensus        97 ~a~~~  101 (101)
T 2la4_A           97 WGKER  101 (101)
T ss_dssp             BCCCC
T ss_pred             eccCC
Confidence            99864

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=7.7e-15  Score=126.27  Aligned_cols=81  Identities=25%  Similarity=0.343  Sum_probs=74.4

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      ....++|||+|||+++|+++|+++|++||. ..|.|+.++ +|+++|||||+|.+.++|.+|++ +|+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            345679999999999999999999999995 599999997 89999999999999999999995 899999999999999


Q ss_pred             CCCC
Q psy3345         413 GKPK  416 (787)
Q Consensus       413 ~~~~  416 (787)
                      +.+.
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8765

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.8e-14  Score=120.60  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=72.1

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||+|||..+|+++|+++|++||.|.++++++         +||||+|.+.++|.+|+..|| +..+.|+.|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~---------~~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   75 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK---------DYAFVHMERAEDAVEAIRGLD-NTEFQGKRMH   75 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS---------SEEEEEESCHHHHHHHHHHHT-TEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC---------CEEEEEECCHHHHHHHHHHhC-CCeeCCcEEE
Confidence            345679999999999999999999999999999999964         399999999999999999997 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.++..
T Consensus        76 V~~a~~~~~   84 (92)
T 2dgt_A           76 VQLSTSRLR   84 (92)
T ss_dssp             EEESSCCCS
T ss_pred             EEEccCCCC
Confidence            999987653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.55  E-value=2.1e-14  Score=123.76  Aligned_cols=83  Identities=17%  Similarity=0.098  Sum_probs=73.4

Q ss_pred             CCCCEEEEecCCc-----cCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         683 QTGSKILVRNIPF-----QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       683 ~~~~~l~V~nLp~-----~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      .++++|+|+||..     .-++++|+++|++||.|.+|+|+++...+++++|||||+|.++++|.+|+..|| |+.+.||
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~ln-G~~~~Gr   84 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLN-GRYFGGR   84 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHT-TCEETTE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHC-CCEECCc
Confidence            4688999999963     237899999999999999999998753347899999999999999999999997 7999999


Q ss_pred             eEEEEEccc
Q psy3345         758 RLVLEWAEE  766 (787)
Q Consensus       758 ~l~v~~A~~  766 (787)
                      .|.|+||.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999975

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.55  E-value=6.2e-15  Score=127.43  Aligned_cols=82  Identities=11%  Similarity=0.270  Sum_probs=76.9

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .+..++.+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+++|+++|||||.|.+.++|++|++  |+..|+|+
T Consensus         4 ~~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~   76 (102)
T 2xs2_A            4 EGKIMPNTVFVGG-----IDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGK   76 (102)
T ss_dssp             CCEEEEEEEEEEC-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTE
T ss_pred             CCCCCCCEEEEeC-----CCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCE
Confidence            3445678899999     9999999999999999999999999999999999999999999999999999  99999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|..+.+
T Consensus        77 ~l~v~~a~~   85 (102)
T 2xs2_A           77 KLKLGPAIR   85 (102)
T ss_dssp             ECEEEEEEE
T ss_pred             EEEEEECCc
Confidence            999999986

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.55  E-value=1.9e-14  Score=127.40  Aligned_cols=78  Identities=17%  Similarity=0.333  Sum_probs=70.5

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceE-EEEEecCHHHHHHHHHHhcCCeeecC--ceEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF-GFVEFITKNEAKRAMKALCQSTHLYG--RRLV  760 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~-afV~F~~~~~A~~Al~~l~~~~~~~G--r~l~  760 (787)
                      +-..|||.||++.+|+++|+++|++||.|.+|+|+.+      .+|| |||+|.+.++|.+|++.|| |..++|  +.|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~------~~gfqAFVef~~~~~A~~Ai~~Ln-G~~i~g~~~~Lr   99 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK------NNQFQALLQYADPVSAQHAKLSLD-GQNIYNACCTLR   99 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE------TTEEEEEEEESCHHHHHHHHHHHT-TCEEETTEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC------CCCcEEEEEECCHHHHHHHHHHcC-CCeecCCCcEEE
Confidence            3456779999999999999999999999999999775      3687 9999999999999999997 799998  9999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||++.+
T Consensus       100 I~~ak~~~  107 (130)
T 3zzy_A          100 IDFSKLTS  107 (130)
T ss_dssp             EEECSCSS
T ss_pred             EEecCCCc
Confidence            99999764

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.55  E-value=1.7e-14  Score=136.47  Aligned_cols=81  Identities=20%  Similarity=0.355  Sum_probs=76.4

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .+...|+|.|     ||+.+|+++|+++|+.||.|..|.|+.++ +|+++|||||.|.+.++|.+||+.||+..|.|+.|
T Consensus        70 ~~~~~l~V~n-----Lp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  144 (165)
T 1rk8_A           70 VEGWILFVTS-----IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI  144 (165)
T ss_dssp             C-CEEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3456799999     99999999999999999999999999986 89999999999999999999999999999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.+|.+
T Consensus       145 ~V~~a~~  151 (165)
T 1rk8_A          145 QVDWCFV  151 (165)
T ss_dssp             EEEESEE
T ss_pred             EEEEecC
Confidence            9999987

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=120.16  Aligned_cols=76  Identities=18%  Similarity=0.218  Sum_probs=70.6

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHh-ccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYF-NNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~-~~~~~~~~~   87 (787)
                      ..+..+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+     +|||||.|.+.++|.+|++.| |+..++|+.
T Consensus         9 ~~~~~~l~V~~-----l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            9 DKTITTLYVGG-----LGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             CSSCCCEEEEC-----CTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCccEEEEcC-----CCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            34667899999     9999999999999999999999999974     799999999999999999999 999999999


Q ss_pred             EEEEEcc
Q psy3345          88 IKVEKCS   94 (787)
Q Consensus        88 i~v~~~~   94 (787)
                      |.|.+|+
T Consensus        79 l~v~~ak   85 (85)
T 2ytc_A           79 LNVKWGR   85 (85)
T ss_dssp             CCEEECC
T ss_pred             EEEEecC
Confidence            9999885

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.54  E-value=2.2e-15  Score=130.00  Aligned_cols=83  Identities=18%  Similarity=0.322  Sum_probs=74.6

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||..+|+++|+++|+.||.|.. .++.+. .+|+++|||||+|.+.++|.+|++ || +..+.|+.|.|+
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~-~~g~~~g~afV~f~~~~~a~~A~~-l~-g~~~~g~~l~V~   90 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LT-GLKVFGNEIKLE   90 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GG-GCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecC-CCCCcCcEEEEEECCHHHHHHHHh-cC-CcEECCcEEEEE
Confidence            36789999999999999999999999999988 565554 578999999999999999999998 97 799999999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||.++..
T Consensus        91 ~a~~~~~   97 (101)
T 1fj7_A           91 KPKGRDG   97 (101)
T ss_dssp             CCSCCCC
T ss_pred             EcCCCCC
Confidence            9987653

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.54  E-value=5.5e-15  Score=126.47  Aligned_cols=79  Identities=22%  Similarity=0.336  Sum_probs=74.5

Q ss_pred             cccceEEEecCcccCCCccCCHHHHH----HHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .++..|+|.|     ||+++|+++|+    ++|+.||.|.+|.|+.  +|+++|||||.|.+.++|.+|++.||+..|.|
T Consensus         6 ~~~~~l~V~n-----Lp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (97)
T 1nu4_A            6 RPNHTIYINN-----LNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   78 (97)
T ss_dssp             CCCSEEEEES-----CCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            4678899999     99999999999    9999999999999874  58899999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|++
T Consensus        79 ~~l~v~~a~~   88 (97)
T 1nu4_A           79 KPMRIQYAKT   88 (97)
T ss_dssp             EECEEEECSS
T ss_pred             cEEEEEEccC
Confidence            9999999987

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=124.91  Aligned_cols=85  Identities=24%  Similarity=0.478  Sum_probs=75.1

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ....+.++|||.|||..+|+++|+++|+.|+   .++++.+. .+|.++|||||+|.+.++|.+||..|| +..+.|++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l   84 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDR-ETGSSKGFGFVDFNSEEDAKAAKEAME-DGEIDGNKV   84 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECS-SSCSEEEEEEEECSSHHHHHHHHHHHT-TCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecC-CCCCcCcEEEEEECCHHHHHHHHHHhC-CCeECCeEE
Confidence            3456789999999999999999999999875   56666664 578999999999999999999999997 699999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||+++..
T Consensus        85 ~V~~a~~~~~   94 (102)
T 2fc8_A           85 TLDWAKPKGE   94 (102)
T ss_dssp             EEEECCCCCS
T ss_pred             EEEEecCCCC
Confidence            9999998764

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.8e-14  Score=124.53  Aligned_cols=80  Identities=16%  Similarity=0.307  Sum_probs=70.7

Q ss_pred             ccCCCCCEEEE--ecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee---
Q psy3345         680 VAKQTGSKILV--RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL---  754 (787)
Q Consensus       680 ~~~~~~~~l~V--~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~---  754 (787)
                      ....+.++|||  .|||..+|+++|+++|++||.|.+|.|+.+       ||||||+|.+.++|.+|+..|| |..+   
T Consensus        20 ~~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-------rgfaFV~f~~~~~A~~Ai~~ln-G~~~~~~   91 (114)
T 2cq2_A           20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-------KPYSFARYRTTEESKRAYVTLN-GKEVVDD   91 (114)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-------CSCEEEEESSHHHHHHHHHHTT-TCEEECT
T ss_pred             CCCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-------CCEEEEEECCHHHHHHHHHHhC-CCEEccc
Confidence            33457889999  559999999999999999999999998653       7999999999999999999997 6877   


Q ss_pred             --cCceEEEEEcccc
Q psy3345         755 --YGRRLVLEWAEEA  767 (787)
Q Consensus       755 --~Gr~l~v~~A~~~  767 (787)
                        .|++|.|.||+..
T Consensus        92 lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           92 LGQKITLYLNFVEKV  106 (114)
T ss_dssp             TSCEEECEEEEESCC
T ss_pred             cCCCcEEEEEecccC
Confidence              6899999999743

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=6.1e-15  Score=130.62  Aligned_cols=85  Identities=20%  Similarity=0.311  Sum_probs=74.3

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      ..+..++..|+|.|     ||+++|+++|+++|+.||.|..|.+..+. +|+++|||||.|.+.++|.+|++.||+..|+
T Consensus        19 ~~~~~~~~~l~V~n-----Lp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   93 (115)
T 2cpx_A           19 YNPGEPNKVLYLKN-----LSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY   93 (115)
T ss_dssp             CCCCSCCSEEEEEC-----CCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCS
T ss_pred             cCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            34455778999999     99999999999999999998544333222 7899999999999999999999999999999


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      |+.|.|.+|++
T Consensus        94 g~~l~v~~a~~  104 (115)
T 2cpx_A           94 GKILVIEFGKN  104 (115)
T ss_dssp             SCBCEEEECCC
T ss_pred             CcEEEEEEccC
Confidence            99999999987

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=2.8e-14  Score=120.04  Aligned_cols=78  Identities=23%  Similarity=0.377  Sum_probs=71.5

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||+|||..+|+++|+++|++||.|.++++++         +||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~---------~~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~   74 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK---------DYAFVHMEKEADAKAAIAQLN-GKEVKGKRIN   74 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS---------SCEEEEESCHHHHHHHHHHHT-TCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC---------CEEEEEECCHHHHHHHHHHhC-CCEECCcEEE
Confidence            345678999999999999999999999999999999964         389999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.+..
T Consensus        75 v~~a~~~~   82 (90)
T 2dnp_A           75 VELSTKGQ   82 (90)
T ss_dssp             EEESCCCC
T ss_pred             EEECCCCC
Confidence            99998764

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=7.1e-15  Score=127.13  Aligned_cols=77  Identities=17%  Similarity=0.160  Sum_probs=70.2

Q ss_pred             CcccceEEEecCcccCCCcc-CCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc--CccCC
Q psy3345           9 VVPRNHISLLDLDEVEFIYK-ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN--TYVFS   85 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~--~~~~~   85 (787)
                      ..|+..|+|+|     ||++ +|++||+++|+.||.|.+|.|+.     ++|||||.|.+.++|.+|++.||+  ..|+|
T Consensus        22 ~~p~~~l~V~N-----Lp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G   91 (112)
T 1x4f_A           22 QELGRVIHLSN-----LPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQG   91 (112)
T ss_dssp             SCCCCEEEEES-----CCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             CCCCCEEEEeC-----CCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            34678899999     9998 99999999999999999999974     489999999999999999999874  56999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      |.|.|.+|..
T Consensus        92 r~l~V~~a~~  101 (112)
T 1x4f_A           92 RCVKVDLSEK  101 (112)
T ss_dssp             SCCEEEEECS
T ss_pred             EEEEEEECcc
Confidence            9999999986

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.54  E-value=4.3e-14  Score=122.27  Aligned_cols=76  Identities=18%  Similarity=0.287  Sum_probs=70.6

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      ..+..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+       +|||||.|.+.++|.+|++.||+..|.|+.|
T Consensus         8 ~~~~~~l~V~n-----l~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l   75 (103)
T 2dgu_A            8 MAKVKVLFVRN-----LANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENI   75 (103)
T ss_dssp             CCCCCCEEEEC-----CCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEE
Confidence            34567899999     99999999999999999999999987       4699999999999999999999999999999


Q ss_pred             EEEEccCC
Q psy3345          89 KVEKCSNL   96 (787)
Q Consensus        89 ~v~~~~~~   96 (787)
                      .|.++++.
T Consensus        76 ~v~~a~~~   83 (103)
T 2dgu_A           76 EIVFAKPP   83 (103)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99999873

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.54  E-value=1.2e-14  Score=125.51  Aligned_cols=78  Identities=13%  Similarity=0.144  Sum_probs=71.1

Q ss_pred             ceEEEecCcccCC----CccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecC----HHH----HHHHHH--H
Q psy3345          13 NHISLLDLDEVEF----IYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHR----EDQ----AQAALD--Y   77 (787)
Q Consensus        13 ~~~~~~~l~~~~l----p~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~----~~~----a~~a~~--~   77 (787)
                      ..|+|.|     |    ||++||++|+++|+.||+|.+|.++.|+ +|+++|||||.|.+    +++    |.+|+.  .
T Consensus         3 ~kI~Vgn-----L~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~   77 (136)
T 2j8a_A            3 CEIVVYP-----AQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHE   77 (136)
T ss_dssp             CEEEEEE-----SSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTT
T ss_pred             cEEEEeC-----CCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhh
Confidence            6799999     9    9999999999999999999999999999 89999999999996    544    899999  7


Q ss_pred             hccCccCCceEEEEEccC
Q psy3345          78 FNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        78 ~~~~~~~~~~i~v~~~~~   95 (787)
                      +|+..|+||.|.|.+-+.
T Consensus        78 lng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           78 SSGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             TTCEEETTEEEEEEECCT
T ss_pred             hcCCeecCcEEEEEECcc
Confidence            899999999999998764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=2e-14  Score=117.16  Aligned_cols=74  Identities=19%  Similarity=0.413  Sum_probs=65.4

Q ss_pred             CCCE-EEEecCCccCcHHH----HHHHHHhc-CCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         684 TGSK-ILVRNIPFQAKQSE----VEELFKAF-GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       684 ~~~~-l~V~nLp~~~t~~d----L~~~F~~~-G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      |..+ |||.|||+.+++++    |+++|++| |.|.+|        +|   |+|||.|.+.++|.+|++.|+ |..++||
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--------tg---G~AfV~F~~~esA~~A~~~l~-G~~l~gr   74 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--------TG---CSAILRFINQDSAERAQKRME-NEDVFGN   74 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--------CT---TCEEEEESSHHHHHHHHHHHT-TCCSSSS
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--------ec---CEEEEEECCHHHHHHHHHHhc-CCccCCc
Confidence            3444 99999999999887    66899999 599777        23   999999999999999999997 7999999


Q ss_pred             eEEEEEcccccc
Q psy3345         758 RLVLEWAEEADN  769 (787)
Q Consensus       758 ~l~v~~A~~~~~  769 (787)
                      +|+|+||+.+.+
T Consensus        75 ~i~v~~A~~~sd   86 (96)
T 2diu_A           75 RIIVSFTPKNRE   86 (96)
T ss_dssp             CCEEESSCCSCC
T ss_pred             eEEEEecCCCcc
Confidence            999999997765

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.53  E-value=1.2e-14  Score=138.48  Aligned_cols=83  Identities=13%  Similarity=0.264  Sum_probs=78.9

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +..++..|+|.|     ||+.+|+++|+++|+.||.|..|.|+.+++|+++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus        84 ~~~~~~~l~V~n-----Lp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~  158 (177)
T 2f3j_A           84 GVETGAKLLVSN-----LDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRP  158 (177)
T ss_dssp             SCTTCEEEEEEC-----CCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSB
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEE
Confidence            445678899999     999999999999999999999999999989999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus       159 l~V~~a~~  166 (177)
T 2f3j_A          159 MDIQLVAS  166 (177)
T ss_dssp             CEEEEESS
T ss_pred             EEEEEecC
Confidence            99999986

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2.4e-14  Score=125.26  Aligned_cols=77  Identities=12%  Similarity=0.181  Sum_probs=72.5

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .+...|+|.|     ||+.+|+++|+++|+.||.|.+|.|+.+     +|||||.|.+.++|.+|++.||+..|+|+.|.
T Consensus        23 ~~~~~l~V~n-----l~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4g_A           23 PKNCTVYCGG-----IASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK   92 (109)
T ss_dssp             SSCCEEEEEC-----CSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3567899999     9999999999999999999999999986     79999999999999999999999999999999


Q ss_pred             EEEccCC
Q psy3345          90 VEKCSNL   96 (787)
Q Consensus        90 v~~~~~~   96 (787)
                      |.+|++.
T Consensus        93 v~~a~~~   99 (109)
T 1x4g_A           93 CYWGKES   99 (109)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9999973

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.53  E-value=1.6e-14  Score=123.36  Aligned_cols=79  Identities=19%  Similarity=0.305  Sum_probs=72.3

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ...++..|+|.|     ||+.+|+++|+++|+.||.|..+    ..+|+++|||||.|.+.++|.+|++.||+..|+|+.
T Consensus        12 ~~~~~~~l~V~n-----L~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   82 (96)
T 1fjc_A           12 KVRAARTLLAKN-----LSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS   82 (96)
T ss_dssp             TTTGGGEEEEES-----CCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE
T ss_pred             cCCCCCEEEEeC-----CCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            344678899999     99999999999999999987666    457999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus        83 l~v~~a~~   90 (96)
T 1fjc_A           83 VSLYYTGE   90 (96)
T ss_dssp             EEEEECSS
T ss_pred             EEEEEcCC
Confidence            99999987

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.53  E-value=1.5e-14  Score=125.98  Aligned_cols=78  Identities=14%  Similarity=0.275  Sum_probs=71.6

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ..+..++.+|+|.|     ||+++|+++|+++|+.||.|.+|.|+       +|||||.|.+.++|.+|++.||+..|+|
T Consensus        25 ~~~~~~~~~l~V~n-----Lp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (108)
T 2jvo_A           25 QEGELSNTRLFVRP-----FPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFAN   92 (108)
T ss_dssp             ---CCSCSEEEECS-----SCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             cCCCCCCCEEEEEC-----CCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            34556778899999     99999999999999999999999998       6999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus        93 ~~l~V~~a~~  102 (108)
T 2jvo_A           93 QPLEVVYSKL  102 (108)
T ss_dssp             EECEEESCSC
T ss_pred             eEEEEEEecC
Confidence            9999999986

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.53  E-value=1.8e-14  Score=132.91  Aligned_cols=89  Identities=18%  Similarity=0.384  Sum_probs=75.0

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEE--Eecccc--CCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFV--RLPKKM--VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY  755 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v--~i~~~~--~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~  755 (787)
                      ....+.++|||+|||+.+|+++|+++|+.||.|.++  +++.+.  ..+|+++|||||+|.+.++|.+|+..|| +..+.
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~ln-g~~~~  118 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEAN-GYVLF  118 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHT-TBEET
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhC-CCEeC
Confidence            445678999999999999999999999999998774  111110  0268899999999999999999999997 79999


Q ss_pred             CceEEEEEcccccc
Q psy3345         756 GRRLVLEWAEEADN  769 (787)
Q Consensus       756 Gr~l~v~~A~~~~~  769 (787)
                      |++|.|+||++...
T Consensus       119 g~~l~V~~a~~~~~  132 (143)
T 3egn_A          119 GKPMVVQFARSARP  132 (143)
T ss_dssp             TEECEEEECCCSCC
T ss_pred             CcEEEEEECCCCCC
Confidence            99999999986544

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.53  E-value=2.7e-14  Score=121.79  Aligned_cols=77  Identities=16%  Similarity=0.329  Sum_probs=70.8

Q ss_pred             CCCcccceEEEecCcccCCCc-cCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIY-KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .+..++.+|+|.|     ||+ ++|+++|+++|+.||.|.+|.|.       +|||||.|.+.++|.+|++.||+..++|
T Consensus        17 ~~~~~~~~l~V~n-----Lp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (97)
T 2xnq_A           17 RGSHMKSRLFIGN-----LPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFG   84 (97)
T ss_dssp             --CCTTCEEEEES-----CCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETT
T ss_pred             CCCCCCCEEEEeC-----CCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3455688899999     999 99999999999999999999983       7999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.++++
T Consensus        85 ~~l~V~~a~~   94 (97)
T 2xnq_A           85 KKLILEVSSS   94 (97)
T ss_dssp             EECEEEECCC
T ss_pred             EEEEEEecCC
Confidence            9999999986

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.6e-14  Score=122.01  Aligned_cols=82  Identities=18%  Similarity=0.280  Sum_probs=73.0

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEE-eccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVR-LPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~-i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ....++|||+|||+.+|+++|+++|+.||.|.+++ |+.+.     ..|.|||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~-----~~~~afV~f~~~~~a~~Ai~~l~-g~~~~g~~l~   85 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-----ETAVVNVTYSSKDQARQALDKLN-GFQLENFTLK   85 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS-----SSEEEEEEESSHHHHHHHHHHHT-TCBCSSCBCE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC-----CCCEEEEEECCHHHHHHHHHHhC-CCEECCcEEE
Confidence            34578999999999999999999999999999995 77763     23449999999999999999997 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.+++.
T Consensus        86 V~~a~~~~~   94 (96)
T 2e44_A           86 VAYIPDEMA   94 (96)
T ss_dssp             EEECCCCCS
T ss_pred             EEEcCcccc
Confidence            999998853

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2e-14  Score=122.86  Aligned_cols=76  Identities=20%  Similarity=0.271  Sum_probs=70.6

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      .+.+|+|.|     ||+.+|+++|+++|+.||.|. +.++.+   +++|||||.|.+.++|++|++.||+..|+|+.|.|
T Consensus        18 ~~~~l~V~n-----L~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   88 (97)
T 2e5j_A           18 LAADVYVGN-----LPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV   88 (97)
T ss_dssp             CCCEEEEEC-----CCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCEEEEeC-----CCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            367899999     999999999999999999987 777753   78999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|++
T Consensus        89 ~~a~~   93 (97)
T 2e5j_A           89 ALARQ   93 (97)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99987

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=5.5e-14  Score=120.64  Aligned_cols=78  Identities=27%  Similarity=0.424  Sum_probs=71.3

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhc--CCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAF--GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~--G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ..+.++|||+|||..+|+++|+++|+.|  |.|.+++++         +|||||+|.+.++|.+|+..|| +..+.|++|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---------~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l   81 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---------RDYAFVHFSNREDAVEAMKALN-GKVLDGSPI   81 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---------SSEEEEEESSHHHHHHHHHHHS-SEEETTEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---------CCeEEEEeCCHHHHHHHHHHhC-CCEeCCcEE
Confidence            4567899999999999999999999999  999998873         5699999999999999999997 799999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||++...
T Consensus        82 ~v~~a~~~~~   91 (99)
T 2cpd_A           82 EVTLAKPVDK   91 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999997653

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.53  E-value=1.2e-14  Score=144.85  Aligned_cols=80  Identities=15%  Similarity=0.275  Sum_probs=75.2

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccC--ceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKG--TVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ...+|+|.|     ||+++|+++|+++|+.||  .|.+|+|++++ +|+++|||||.|.+.++|.+||+.||+..|.||.
T Consensus        67 ~~~~lfVgn-----L~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~  141 (229)
T 3q2s_C           67 KRIALYIGN-----LTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN  141 (229)
T ss_dssp             --CEEEEES-----CCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBC
T ss_pred             CccEEEEeC-----CCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEE
Confidence            456699999     999999999999999999  99999999997 8999999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|++
T Consensus       142 l~V~~a~~  149 (229)
T 3q2s_C          142 PVVTPVNK  149 (229)
T ss_dssp             CEEEECCH
T ss_pred             eEEEECCC
Confidence            99999986

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.53  E-value=3.6e-15  Score=128.68  Aligned_cols=78  Identities=19%  Similarity=0.287  Sum_probs=71.9

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      +..+|+|.|     ||+++|+++|+++|+.||.|.. .++.++ +|+++|||||.|.+.++|.+||+ ||+..|.|+.|.
T Consensus        16 ~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~   88 (101)
T 1fj7_A           16 TPFNLFIGN-----LNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK   88 (101)
T ss_dssp             CSEEEEEEC-----CCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEE
Confidence            567899999     9999999999999999998888 555554 79999999999999999999999 999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|++
T Consensus        89 V~~a~~   94 (101)
T 1fj7_A           89 LEKPKG   94 (101)
T ss_dssp             EECCSC
T ss_pred             EEEcCC
Confidence            999987

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.53  E-value=2.2e-14  Score=124.88  Aligned_cols=79  Identities=25%  Similarity=0.541  Sum_probs=72.1

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ...+.++|||+|||..+|+++|+++|++||.|.+++++         +|||||+|.+.++|.+|+..|| +..+.|++|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---------kg~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~   96 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---------NGFAFVEFEEAESAAKAIEEVH-GKSFANQPLE   96 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---------TTEEEEECSSHHHHHHHHHHHT-TCEETTEECE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---------CCEEEEEECCHHHHHHHHHHcC-CCEECCeEEE
Confidence            34578999999999999999999999999999999986         5899999999999999999997 7999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.+...
T Consensus        97 V~~a~~~~~  105 (108)
T 2jvo_A           97 VVYSKLPAK  105 (108)
T ss_dssp             EESCSCCC-
T ss_pred             EEEecCCCC
Confidence            999987653

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.52  E-value=1.5e-14  Score=123.56  Aligned_cols=80  Identities=21%  Similarity=0.493  Sum_probs=72.5

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|+.||.|..+    .  .+|.++|||||+|.+.++|.+|+..|+ +..+.|++|.|
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~--~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v   85 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----S--QDGKSKGIAYIEFKSEADAEKNLEEKQ-GAEIDGRSVSL   85 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----E--ETTEEEEEEEEEESSHHHHHHHHHHTT-EEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----C--CCCCcceEEEEEECCHHHHHHHHHHhC-CCEECCeEEEE
Confidence            3467899999999999999999999999988766    2  378899999999999999999999997 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      +||.++.
T Consensus        86 ~~a~~~~   92 (96)
T 1fjc_A           86 YYTGEKG   92 (96)
T ss_dssp             EECSSSC
T ss_pred             EEcCCCC
Confidence            9998765

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.52  E-value=7.5e-15  Score=118.98  Aligned_cols=75  Identities=24%  Similarity=0.397  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      +|||+|||+++|+++|+++|++||+|..+.++.++.+|.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999998889999999999999999999998 5889999999998764

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=3.2e-14  Score=122.10  Aligned_cols=76  Identities=20%  Similarity=0.300  Sum_probs=71.6

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .+..+|+|.|     ||+.+|+++|+++|+.||.|.+|+|+.+     +|||||.|.+.++|.+|++.||+..|.|+.|.
T Consensus        13 ~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~   82 (99)
T 2cpj_A           13 TQRSRLFVGN-----LPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLR   82 (99)
T ss_dssp             CCTTEEEEES-----CCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCE
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEE
Confidence            4567899999     9999999999999999999999999854     79999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.++++
T Consensus        83 v~~a~~   88 (99)
T 2cpj_A           83 VRFACH   88 (99)
T ss_dssp             EEESSC
T ss_pred             EEEcCC
Confidence            999987

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.52  E-value=3.6e-14  Score=118.76  Aligned_cols=79  Identities=29%  Similarity=0.472  Sum_probs=63.3

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-CeeecCceE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-STHLYGRRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-~~~~~Gr~l  759 (787)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|+++      +||||||+|.+.++|.+    +++ ...+.|++|
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~------srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v   76 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP------FRAFAFVTFADDKVAQS----LCGEDLIIKGISV   76 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS------CCSEEEEEESCHHHHHH----HTTCEEEETTEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC------CCCEEEEEECCHHHHHH----HcCCCcccCCEEE
Confidence            3457899999999999999999999999999999999886      79999999999999983    332 233559999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|.+|.++..
T Consensus        77 ~v~~a~~k~~   86 (89)
T 3d2w_A           77 HISNAEPKHN   86 (89)
T ss_dssp             EEEECC----
T ss_pred             EEEEcCCCCc
Confidence            9999997653

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=2.2e-14  Score=122.34  Aligned_cols=76  Identities=17%  Similarity=0.400  Sum_probs=70.1

Q ss_pred             CCcccceEEEecCcccCCCc-cCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIY-KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ...++.+|+|.|     ||+ .+|+++|+++|+.||.|.+|.|.       +|||||.|.+.++|.+|++.||+..+.|+
T Consensus         6 ~~~~~~~l~V~n-----lp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   73 (96)
T 2kvi_A            6 NIPPKSRLFIGN-----LPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGK   73 (96)
T ss_dssp             ---CCEEEEEES-----STTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTT
T ss_pred             cCCCCCEEEEeC-----CCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            345688899999     999 99999999999999999999994       68999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.++++
T Consensus        74 ~l~V~~a~~   82 (96)
T 2kvi_A           74 KLILEVSSS   82 (96)
T ss_dssp             TBCEEEEEC
T ss_pred             EEEEEEcCc
Confidence            999999987

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.52  E-value=1e-14  Score=145.26  Aligned_cols=83  Identities=16%  Similarity=0.299  Sum_probs=76.9

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcC--CeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G--~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..++|||.|||+.+|+++|+++|+.||  .|.+|+|+++. .+|+++|||||+|.+.++|.+||..|| +..|.|+.|+|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~-~tg~skGfaFV~f~~~~~a~~Ai~~ln-g~~~~Gr~l~V  144 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR-ANGQSKGFALVGVGSEASSKKLMDLLP-KRELHGQNPVV  144 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECT-TTCCEEEEEEEEESCTTHHHHHHTTST-TSCBTTBCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecC-CCCccceEEEEEECCHHHHHHHHHHcC-CCeECCEEeEE
Confidence            567999999999999999999999999  99999999985 689999999999999999999999997 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      .||.+..
T Consensus       145 ~~a~~~~  151 (229)
T 3q2s_C          145 TPVNKQF  151 (229)
T ss_dssp             EECCHHH
T ss_pred             EECCCCc
Confidence            9998655

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=1.9e-14  Score=122.75  Aligned_cols=78  Identities=18%  Similarity=0.504  Sum_probs=71.0

Q ss_pred             CCCCCEEEEecCCc-cCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         682 KQTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~-~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ..+.++|||+|||. .+|+++|+++|++||.|.+++|+         +|||||+|.+.++|..|+..|+ +..+.|++|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~---------~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~   76 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---------NAFGFIQFDNPQSVRDAIECES-QEMNFGKKLI   76 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---------TTEEEEEESCHHHHHHHHHHHT-CSSCBTTTBC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---------CCEEEEEECCHHHHHHHHHHcC-CCeeCCcEEE
Confidence            35788999999998 99999999999999999999983         6799999999999999999997 6999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.+...
T Consensus        77 V~~a~~~~~   85 (96)
T 2kvi_A           77 LEVSSSNAR   85 (96)
T ss_dssp             EEEEECCCC
T ss_pred             EEEcCcCCC
Confidence            999987654

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.52  E-value=3.3e-14  Score=130.80  Aligned_cols=79  Identities=15%  Similarity=0.263  Sum_probs=71.2

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC--ceEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG--RRLVL  761 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G--r~l~v  761 (787)
                      ...+|||.|||+.+|+++|+++|++||.|.+|+|..+     .++|||||+|.+.++|..|+..|| |..|+|  ++|+|
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k-----~~rgfAFVeF~d~~~A~~Ai~~Ln-G~~i~g~g~~L~V  118 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLD-GQNIYNACCTLRI  118 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES-----SSCEEEEEEESCHHHHHHHHHHST-TBCSSSSCSCEEE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCCEEEEEECCHHHHHHHHHHhC-CCEecCCCcEEEE
Confidence            3466889999999999999999999999999999654     257999999999999999999997 799976  99999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      +||++++
T Consensus       119 ~~Ak~~~  125 (164)
T 1sjr_A          119 DFSKLTS  125 (164)
T ss_dssp             EECSSSS
T ss_pred             EEecCCc
Confidence            9999775

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=1.7e-14  Score=124.39  Aligned_cols=76  Identities=14%  Similarity=0.112  Sum_probs=71.0

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ..+..|+|.|     ||+++|+++|+++|+.||.|.+|+|+     +++|||||.|.+.++|.+|+..||+..|+|+.|.
T Consensus        25 ~~~~~l~V~n-----lp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   94 (101)
T 2la4_A           25 PRVTTAYIGN-----IPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLR   94 (101)
T ss_dssp             SSCCEEEEES-----CCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECC
T ss_pred             CCCCEEEEcC-----CCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3467899999     99999999999999999999999998     4589999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|++
T Consensus        95 V~~a~~  100 (101)
T 2la4_A           95 TGWGKE  100 (101)
T ss_dssp             CCBCCC
T ss_pred             EEeccC
Confidence            999875

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.3e-14  Score=121.43  Aligned_cols=79  Identities=15%  Similarity=0.243  Sum_probs=71.7

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCc-eEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc-Ccc
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGT-VTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN-TYV   83 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~-~~~   83 (787)
                      |++..+..+|+|.|     ||+++|+++|+++|+.||. |..+.+.      ++|||||.|.+.++|.+|++.||+ ..|
T Consensus         2 s~~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~   70 (93)
T 2cqh_A            2 SSGSSGMNKLYIGN-----LSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVEL   70 (93)
T ss_dssp             CCCCCCCCCEEEEC-----CCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEE
T ss_pred             CCCCCCCcEEEEeC-----CCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeE
Confidence            45566788899999     9999999999999999998 6777663      479999999999999999999999 999


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +|+.|.|.+|++
T Consensus        71 ~g~~l~v~~a~~   82 (93)
T 2cqh_A           71 HGKIMEVDYSVS   82 (93)
T ss_dssp             TTEECEEEECCC
T ss_pred             CCEEEEEEEccC
Confidence            999999999987

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.51  E-value=5.3e-14  Score=121.20  Aligned_cols=81  Identities=16%  Similarity=0.132  Sum_probs=72.3

Q ss_pred             cccceEEEecCcccCCCc-----cCCHHHHHHHhhccCceEEEEEEecC--CCCcceEEEEEecCHHHHHHHHHHhccCc
Q psy3345          10 VPRNHISLLDLDEVEFIY-----KITQEQLKAKFEEKGTVTDVQLKYTT--EGKFRRFAFIGYHREDQAQAALDYFNNTY   82 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~-----~~~~~~l~~~f~~~g~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~~~~~~~   82 (787)
                      .|+..|.|+|     |..     .-+++||+++|++||.|.+|+|+.++  .|+++|||||.|.++++|.+|++.|||..
T Consensus         6 ~~s~~l~l~N-----m~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~   80 (105)
T 2pe8_A            6 CPTKVVLLRN-----MVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRY   80 (105)
T ss_dssp             SCCSEEEEES-----SSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEEc-----CCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCE
Confidence            4677899999     642     34899999999999999999999986  37899999999999999999999999999


Q ss_pred             cCCceEEEEEccC
Q psy3345          83 VFSSRIKVEKCSN   95 (787)
Q Consensus        83 ~~~~~i~v~~~~~   95 (787)
                      ++||.|.|.++.+
T Consensus        81 ~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           81 FGGRVVKACFYNL   93 (105)
T ss_dssp             ETTEECEEEECCH
T ss_pred             ECCcEEEEEEcCH
Confidence            9999999999975

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.51  E-value=8.8e-15  Score=126.05  Aligned_cols=70  Identities=16%  Similarity=0.302  Sum_probs=66.4

Q ss_pred             CCCccCCHHHHHHHh------------hccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          24 EFIYKITQEQLKAKF------------EEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        24 ~lp~~~~~~~l~~~f------------~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      |||+.+|+++|+++|            ++||.|.+|.|+.++.|+++|||||.|.++++|.+|++.|||..++||.|.|.
T Consensus        22 ~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~  101 (104)
T 1jmt_A           22 GLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE  101 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEE
Confidence            499999999888877            99999999999998889999999999999999999999999999999999999


Q ss_pred             Ec
Q psy3345          92 KC   93 (787)
Q Consensus        92 ~~   93 (787)
                      ++
T Consensus       102 ~s  103 (104)
T 1jmt_A          102 LS  103 (104)
T ss_dssp             EC
T ss_pred             Ec
Confidence            86

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.26  E-value=1.3e-15  Score=135.17  Aligned_cols=85  Identities=20%  Similarity=0.289  Sum_probs=78.6

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeE--------EEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL  754 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~--------v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~  754 (787)
                      .+.++|||+|||..+|+++|+++|++||.|.+        |+|+.+. .+|+++|||||+|.+.++|.+|+..|| +..+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~   82 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR-ETGKLKGEATVSFDDPPSAKAAIDWFD-GKEF   82 (116)
Confidence            46789999999999999999999999999998        8898885 578999999999999999999999997 7999


Q ss_pred             cCceEEEEEcccccc
Q psy3345         755 YGRRLVLEWAEEADN  769 (787)
Q Consensus       755 ~Gr~l~v~~A~~~~~  769 (787)
                      .|++|.|+||.++..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999997654

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.51  E-value=2.9e-14  Score=125.04  Aligned_cols=77  Identities=26%  Similarity=0.491  Sum_probs=70.6

Q ss_pred             CCCCCEEEEecCCcc-CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         682 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~-~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      ....++|||.|||.. +|+++|+++|++||.|..|+|         ++|||||+|.+.++|.+|+..|+ +..+.|++|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---------~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~   93 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---------HKGYAFVQYSNERHARAAVLGEN-GRVLAGQTLD   93 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---------ETTEEEEECSSSHHHHHHHHHHT-TCEETTEECC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---------eCCEEEEEECCHHHHHHHHHHcC-CCEECCeEEE
Confidence            345689999999999 999999999999999999998         36899999999999999999997 7999999999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |+||.+..
T Consensus        94 V~~a~~~~  101 (110)
T 1wf1_A           94 INMAGEPK  101 (110)
T ss_dssp             EEESCCCC
T ss_pred             EEECCCCC
Confidence            99998543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.51  E-value=8.8e-15  Score=126.47  Aligned_cols=84  Identities=21%  Similarity=0.482  Sum_probs=75.9

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||..+|+++|+++|+.||.|.+|+|+.+.  +|.++|||||+|.+.++|.+|+.  + +..+.|+.|.|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~a~~Ai~--~-~~~~~g~~l~v~   81 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR--TGVSKGYGFVSFYNDVDVQKIVE--S-QINFHGKKLKLG   81 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT--TSCEEEEEEEEESSCCCHHHHTT--C-CCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC--CCCccceEEEEECCHHHHHHHHh--C-CCeECCEEEEEE
Confidence            356899999999999999999999999999999999984  89999999999999999999999  5 799999999999


Q ss_pred             EccccccHH
Q psy3345         763 WAEEADNVE  771 (787)
Q Consensus       763 ~A~~~~~~~  771 (787)
                      +|.++....
T Consensus        82 ~a~~~~~~~   90 (102)
T 2xs2_A           82 PAIRKQNLS   90 (102)
T ss_dssp             EEEECC---
T ss_pred             ECCcCcchh
Confidence            999777653

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.50  E-value=1.7e-14  Score=128.14  Aligned_cols=82  Identities=20%  Similarity=0.359  Sum_probs=73.4

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCee--EEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~--~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      ....++|||+|||+.+|+++|+++|+.| .|.  +|+|+++.  .|+++|||||+|.+.++|.+||.. + +..+.||.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~--~GrsrGfaFV~F~~~e~A~~Al~~-~-~~~l~gR~I  113 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP--EGKITGEAFVQFASQELAEKALGK-H-KERIGHRYI  113 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS--SSSSCSEEEEEESSTTHHHHHHTT-T-TCCBTTBCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC--CCCCceEEEEEECCHHHHHHHHHH-C-CCEECCEEE
Confidence            3467899999999999999999999999 577  89999985  599999999999999999999985 4 589999999


Q ss_pred             EEEEccccc
Q psy3345         760 VLEWAEEAD  768 (787)
Q Consensus       760 ~v~~A~~~~  768 (787)
                      .|.+|.+++
T Consensus       114 ~V~~a~~~e  122 (126)
T 2hgm_A          114 EVFKSSQEE  122 (126)
T ss_dssp             CCEEECHHH
T ss_pred             EEEECCHHH
Confidence            999997543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=6e-14  Score=119.71  Aligned_cols=84  Identities=19%  Similarity=0.190  Sum_probs=73.6

Q ss_pred             CCCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEE-EEEecCCCCcceEEEEEecCHHHHHHHHHHhccCc
Q psy3345           4 HLSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDV-QLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY   82 (787)
Q Consensus         4 ~~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~   82 (787)
                      ++..+...+.+|+|.|     ||+++|+++|+++|+.||.|.+| .|+.++.   .|.|||.|.+.++|.+|++.||+..
T Consensus         7 ~~~~~~~~~~~l~V~n-----lp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~   78 (96)
T 2e44_A            7 GSVPKRQRIRKLQIRN-----IPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQ   78 (96)
T ss_dssp             SCCCCCCSCCCEEEEE-----ECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCCCCEEEEEc-----CCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCE
Confidence            3344445577899999     99999999999999999999999 5777643   3349999999999999999999999


Q ss_pred             cCCceEEEEEccC
Q psy3345          83 VFSSRIKVEKCSN   95 (787)
Q Consensus        83 ~~~~~i~v~~~~~   95 (787)
                      |+||.|.|.+|.+
T Consensus        79 ~~g~~l~V~~a~~   91 (96)
T 2e44_A           79 LENFTLKVAYIPD   91 (96)
T ss_dssp             CSSCBCEEEECCC
T ss_pred             ECCcEEEEEEcCc
Confidence            9999999999987

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=4.3e-14  Score=123.80  Aligned_cols=83  Identities=58%  Similarity=0.984  Sum_probs=77.4

Q ss_pred             cCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCccc
Q psy3345         444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  523 (787)
Q Consensus       444 ~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~  523 (787)
                      ....++|+|+|||+.+++++|+++|++||.|..|.+++++++|||+|.+.++|.+|+..|||..+.|++|.|+|++...+
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   86 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVF   86 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCcc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999988866


Q ss_pred             ccc
Q psy3345         524 AEA  526 (787)
Q Consensus       524 ~~~  526 (787)
                      ...
T Consensus        87 ~~~   89 (111)
T 1whx_A           87 GAA   89 (111)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.50  E-value=2.4e-14  Score=132.13  Aligned_cols=85  Identities=22%  Similarity=0.319  Sum_probs=75.0

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEE------EEEecCCCCcceEEEEEecCHHHHHHHHHHhc
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDV------QLKYTTEGKFRRFAFIGYHREDQAQAALDYFN   79 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~------~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~   79 (787)
                      ..+..++.+|+|.|     ||+++|+++|+++|+.||.|..|      .+....+|+++|||||.|.+.++|.+|+..||
T Consensus        39 ~~~~~~~~~l~V~n-----Lp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~ln  113 (143)
T 3egn_A           39 YEPGEPNCRIYVKN-----LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEAN  113 (143)
T ss_dssp             CCCCSCCSEEEEEE-----ECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHT
T ss_pred             cCCCCCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhC
Confidence            34566788999999     99999999999999999988764      22222469999999999999999999999999


Q ss_pred             cCccCCceEEEEEccC
Q psy3345          80 NTYVFSSRIKVEKCSN   95 (787)
Q Consensus        80 ~~~~~~~~i~v~~~~~   95 (787)
                      +..|.|+.|.|.+|++
T Consensus       114 g~~~~g~~l~V~~a~~  129 (143)
T 3egn_A          114 GYVLFGKPMVVQFARS  129 (143)
T ss_dssp             TBEETTEECEEEECCC
T ss_pred             CCEeCCcEEEEEECCC
Confidence            9999999999999986

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.50  E-value=6.3e-14  Score=122.82  Aligned_cols=77  Identities=16%  Similarity=0.295  Sum_probs=71.6

Q ss_pred             CCCcccceEEEecCcccCCCcc-CCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYK-ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .|..++.+|+|.|     ||+. +|+++|+++|+.||.|.+|.|       ++|||||.|.+.++|.+|++.||+..|+|
T Consensus        22 ~~~~~~~~l~V~n-----l~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g   89 (110)
T 1wf1_A           22 DPKSINSRVFIGN-----LNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAG   89 (110)
T ss_dssp             CCTTCSSEEEECS-----CCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCcEEEEeC-----CCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3445567899999     9999 999999999999999999999       57999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|++
T Consensus        90 ~~l~V~~a~~   99 (110)
T 1wf1_A           90 QTLDINMAGE   99 (110)
T ss_dssp             EECCEEESCC
T ss_pred             eEEEEEECCC
Confidence            9999999986

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=1.4e-13  Score=118.18  Aligned_cols=77  Identities=18%  Similarity=0.343  Sum_probs=70.6

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhcc--CceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEK--GTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      ...+..+|+|.|     ||+++|+++|+++|+.|  |.|..|+++       +|||||.|.+.++|.+|++.||+..|.|
T Consensus        11 ~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (99)
T 2cpd_A           11 TMSSVKILYVRN-----LMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDG   78 (99)
T ss_dssp             CSSCCCEEEEES-----CCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETT
T ss_pred             ccCCcCEEEEeC-----CCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            344677899999     99999999999999999  899999875       5799999999999999999999999999


Q ss_pred             ceEEEEEccCC
Q psy3345          86 SRIKVEKCSNL   96 (787)
Q Consensus        86 ~~i~v~~~~~~   96 (787)
                      +.|.|.+|++.
T Consensus        79 ~~l~v~~a~~~   89 (99)
T 2cpd_A           79 SPIEVTLAKPV   89 (99)
T ss_dssp             EEEEEECCCCC
T ss_pred             cEEEEEECCCC
Confidence            99999999873

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.49  E-value=6e-14  Score=133.69  Aligned_cols=85  Identities=31%  Similarity=0.450  Sum_probs=78.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..++++|||.|||..+|+++|+++|+.||.|.+|.|+.+.  +|.++|||||+|.+.++|.+|+..|| +..+.|+.|.|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~--~g~~kG~afV~F~~~~~A~~Ai~~ln-g~~l~Gr~l~V  161 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR--SGRSLGTADVHFERRADALKAMKQYK-GVPLDGRPMDI  161 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT--TSSCSCCEEEEESCHHHHHHHHHHST-TCBCSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC--CCCEeeEEEEEeCCHHHHHHHHHHhC-CCEECCEEEEE
Confidence            3567899999999999999999999999999999999984  89999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.+...
T Consensus       162 ~~a~~~~~  169 (177)
T 2f3j_A          162 QLVASQID  169 (177)
T ss_dssp             EEESSGGG
T ss_pred             EEecCCCC
Confidence            99986543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=1.4e-13  Score=117.49  Aligned_cols=78  Identities=18%  Similarity=0.277  Sum_probs=70.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.||  .+|+++|+++|++||.|.+|+|..       ++|||||+|.+.++|.+|+..|| +..+.|++|.|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~-------~~g~afV~f~~~~~a~~Ai~~l~-g~~~~g~~l~v   81 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMESADQAVAELN-GTQVESVQLKV   81 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEET-------TTTEEEEEESSHHHHHHHHHHTT-TEEETTEEEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecC-------CCCEEEEEECCHHHHHHHHHHhC-CCeECCeEEEE
Confidence            456789999996  899999999999999999999853       58999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++..
T Consensus        82 ~~a~~~~~   89 (97)
T 1x5p_A           82 NIARKQPM   89 (97)
T ss_dssp             ECCSSCCC
T ss_pred             EECCCCCC
Confidence            99987654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.23  E-value=2.3e-15  Score=133.50  Aligned_cols=81  Identities=22%  Similarity=0.324  Sum_probs=76.3

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEE--------EEEEecC-CCCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD--------VQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      .++.+|+|.|     ||+++|+++|+++|+.||.|.+        |.|+.++ +|+++|||||.|.+.++|.+|++.||+
T Consensus         5 ~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   79 (116)
T 2lcw_A            5 SDNNTIFVQG-----LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   79 (116)
Confidence            3567889999     9999999999999999999998        9999986 699999999999999999999999999


Q ss_pred             CccCCceEEEEEccC
Q psy3345          81 TYVFSSRIKVEKCSN   95 (787)
Q Consensus        81 ~~~~~~~i~v~~~~~   95 (787)
                      ..|+|+.|.|.+|++
T Consensus        80 ~~~~g~~l~V~~a~~   94 (116)
T 2lcw_A           80 KEFSGNPIKVSFATR   94 (116)
Confidence            999999999999987

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.9e-14  Score=119.41  Aligned_cols=79  Identities=20%  Similarity=0.315  Sum_probs=70.1

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCC-eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCC-eeecCceE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS-THLYGRRL  759 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~-I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~-~~~~Gr~l  759 (787)
                      ..+.++|||.|||..+|+++|+++|++||. |..+.+.        ++|||||+|.+.++|.+|+..|| + ..+.|++|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~--------~~g~afV~f~~~~~A~~A~~~l~-g~~~~~g~~l   75 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--------KSGYAFVDYPDQNWAIRAIETLS-GKVELHGKIM   75 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE--------ETTEEEECCSCHHHHHHHHHHHT-TTCEETTEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc--------CCCEEEEEECCHHHHHHHHHHcc-CCeeECCEEE
Confidence            346789999999999999999999999999 6656552        47899999999999999999997 7 89999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      .|+||.++..
T Consensus        76 ~v~~a~~~~~   85 (93)
T 2cqh_A           76 EVDYSVSKKL   85 (93)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCccc
Confidence            9999997654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.49  E-value=9e-14  Score=122.73  Aligned_cols=74  Identities=20%  Similarity=0.321  Sum_probs=66.9

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceE-EEEEecCHHHHHHHHHHhcCCeeecC--ceEEEEE
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF-GFVEFITKNEAKRAMKALCQSTHLYG--RRLVLEW  763 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~-afV~F~~~~~A~~Al~~l~~~~~~~G--r~l~v~~  763 (787)
                      .|||.|||+.+|+++|+++|++||.|.+|+|+..       .|| |||+|.+.++|..|++.|| |..|+|  +.|+|+|
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-------~Gf~aFVef~~~~~A~~A~~~Ln-G~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-------NGIQAMVEFESVLCAQKAKAALN-GADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-------SSEEEEEEESSHHHHHHHHHHHT-TCCCBTTBSEEEEEC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-------CCCEEEEEECCHHHHHHHHHHhC-CCEecCCCeEEEEEE
Confidence            4579999999999999999999999999999653       286 9999999999999999997 799988  6999999


Q ss_pred             ccccc
Q psy3345         764 AEEAD  768 (787)
Q Consensus       764 A~~~~  768 (787)
                      |++..
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            99775

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.49  E-value=6.2e-14  Score=117.33  Aligned_cols=76  Identities=24%  Similarity=0.473  Sum_probs=70.2

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||..+|+++|+++|++| .|.++++.       +++|||||+|.+.++|.+|+..|| +..+.|++|+|+|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-------~~~g~afV~f~~~~~a~~Ai~~l~-g~~~~g~~l~V~~   74 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-------RNKRTAFVTLLNGEQAQNAIQMFH-QYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-------GGGTEEEECCSCHHHHHHHHHHHT-TEEETTEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-------CCCcEEEEEECCHHHHHHHHHHhC-CCeECCcEEEEEE
Confidence            46789999999999999999999999 89999985       368999999999999999999997 7999999999999


Q ss_pred             ccccc
Q psy3345         764 AEEAD  768 (787)
Q Consensus       764 A~~~~  768 (787)
                      |..+.
T Consensus        75 a~~~~   79 (88)
T 1wg1_A           75 QPTDA   79 (88)
T ss_dssp             CCCCC
T ss_pred             cCCCc
Confidence            97654

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.48  E-value=5.9e-14  Score=117.48  Aligned_cols=74  Identities=14%  Similarity=0.170  Sum_probs=69.7

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      .+.+|+|.|     ||+++|+++|+++|+.| .|.+|+|.     +++|||||.|.+.++|.+|++.||+..++|++|.|
T Consensus         4 ~~~~l~V~n-----Lp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   72 (88)
T 1wg1_A            4 GSSGILVKN-----LPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV   72 (88)
T ss_dssp             CCCCEEEES-----CCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEE
Confidence            467799999     99999999999999999 99999985     67999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|..
T Consensus        73 ~~a~~   77 (88)
T 1wg1_A           73 QLQPT   77 (88)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99975

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.48  E-value=7.8e-14  Score=120.36  Aligned_cols=79  Identities=18%  Similarity=0.242  Sum_probs=71.7

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcC----HHH----HHHHHH--HhCCce
Q psy3345         337 GRIFVRNL----SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM----PEH----ATQAYQ--HLDGTV  402 (787)
Q Consensus       337 ~~l~V~nL----p~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~----~~~----A~~a~~--~l~~~~  402 (787)
                      ..|||+||    |+.+++.+|+++|+.||+|.++.++.|+.||.++|||||+|.+    +++    |.+|+.  .++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    9999999999999999999999999999999999999999996    433    889988  789999


Q ss_pred             eCCeEEEEeeCCC
Q psy3345         403 FLGRMLHLIPGKP  415 (787)
Q Consensus       403 ~~g~~l~v~~~~~  415 (787)
                      |.|+.|+|..-..
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998653

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=1.7e-13  Score=116.33  Aligned_cols=77  Identities=18%  Similarity=0.195  Sum_probs=68.4

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ..-...+|+|.|     ||+++|+++|+++|+.||.|.+|  +.++ +|+   ||||.|.+.++|.+|+. ||+..|+|+
T Consensus         4 ~~~~~~~l~V~n-----l~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~   72 (94)
T 2e5g_A            4 GSSGLRSVFVSG-----FPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGH   72 (94)
T ss_dssp             CCTTCCEEEEEC-----CCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTE
T ss_pred             ccCCCCEEEEEC-----CCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCE
Confidence            344567899999     99999999999999999999987  4444 454   99999999999999999 999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.++.+
T Consensus        73 ~l~V~~a~~   81 (94)
T 2e5g_A           73 RLRVRPREQ   81 (94)
T ss_dssp             ECCCBCSCC
T ss_pred             EEEEEECCc
Confidence            999998876

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=2.9e-13  Score=119.46  Aligned_cols=80  Identities=19%  Similarity=0.247  Sum_probs=68.8

Q ss_pred             CCCCcccce--EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceE-EEEEecCHHHHHHHHHHhccCc
Q psy3345           6 SGPVVPRNH--ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRF-AFIGYHREDQAQAALDYFNNTY   82 (787)
Q Consensus         6 ~~~~~~~~~--~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~-afv~f~~~~~a~~a~~~~~~~~   82 (787)
                      .+|..|+..  |+|.|     |||.+|+++|+++|+.||.|.+|.|.. +    .|| |||.|.+.++|..|++.|||..
T Consensus        17 ~~~~~ps~vl~l~V~N-----L~~~vt~~~L~~~Fs~yG~V~~v~i~~-~----~Gf~aFVef~~~~~A~~A~~~LnG~~   86 (124)
T 2e5i_A           17 DDPSGGNKVLLLSIQN-----PLYPITVDVLYTVCNPVGKVQRIVIFK-R----NGIQAMVEFESVLCAQKAKAALNGAD   86 (124)
T ss_dssp             CCCCCCCSEEEEEEES-----CCSCCCHHHHHHHHTTTSCEEEEEEEE-S----SSEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCcEEEEEEcC-----cCCCCCHHHHHHHHHhcCCEEEEEEEe-C----CCCEEEEEECCHHHHHHHHHHhCCCE
Confidence            345555544  34677     999999999999999999999999965 2    386 9999999999999999999999


Q ss_pred             cCC--ceEEEEEccC
Q psy3345          83 VFS--SRIKVEKCSN   95 (787)
Q Consensus        83 ~~~--~~i~v~~~~~   95 (787)
                      |.|  +.|.|.+|++
T Consensus        87 i~g~~~~l~V~~Ak~  101 (124)
T 2e5i_A           87 IYAGCCTLKIEYARP  101 (124)
T ss_dssp             CBTTBSEEEEECCSC
T ss_pred             ecCCCeEEEEEEecC
Confidence            987  6999999987

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=2.7e-13  Score=115.74  Aligned_cols=76  Identities=24%  Similarity=0.337  Sum_probs=69.8

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +..+..+|+|.|     |  ++|+++|+++|+.||.|.+|.|.     +++|||||.|.+.++|.+||..||+..|.|+.
T Consensus        11 ~~~~~~~l~V~n-----~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   78 (97)
T 1x5p_A           11 APRKGNTLYVYG-----E--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQ   78 (97)
T ss_dssp             CCCCCSEEEEEC-----S--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEE
T ss_pred             CCCCCCEEEEcC-----C--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            344667899999     6  89999999999999999999994     56899999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus        79 l~v~~a~~   86 (97)
T 1x5p_A           79 LKVNIARK   86 (97)
T ss_dssp             EEEECCSS
T ss_pred             EEEEECCC
Confidence            99999987

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.46  E-value=1.1e-13  Score=115.68  Aligned_cols=77  Identities=19%  Similarity=0.273  Sum_probs=63.3

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCc--c
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY--V   83 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~--~   83 (787)
                      +.+..+...|+|.|     ||+++||++|+++|+.||.|.+|+|+.+    ++|||||+|.+.++|.+    +++..  +
T Consensus         5 ~~~~~~~~~l~V~~-----Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~   71 (89)
T 3d2w_A            5 HHHHHHGSKVFVGR-----CTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLII   71 (89)
T ss_dssp             ------CCEEEEES-----CCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEE
T ss_pred             CCCCCCCCEEEEeC-----CCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCccc
Confidence            34566788899999     9999999999999999999999999874    79999999999999984    35554  5


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +|+.|.|..|.+
T Consensus        72 ~g~~v~v~~a~~   83 (89)
T 3d2w_A           72 KGISVHISNAEP   83 (89)
T ss_dssp             TTEEEEEEECC-
T ss_pred             CCEEEEEEEcCC
Confidence            699999999986

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.46  E-value=1.8e-13  Score=125.95  Aligned_cols=73  Identities=18%  Similarity=0.239  Sum_probs=66.6

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC--ceEEEEE
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS--SRIKVEK   92 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~--~~i~v~~   92 (787)
                      |+|.|     |||.+|+++|+++|+.||.|.+|.|..+   +++|||||.|.+.++|.+|++.|||..|.|  +.|.|++
T Consensus        49 l~VgN-----L~~~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           49 IIVEN-----LFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             EEECS-----CCSCCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             EEEeC-----cCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            55666     9999999999999999999999998653   368999999999999999999999999955  9999999


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      |++
T Consensus       121 Ak~  123 (164)
T 1sjr_A          121 SKL  123 (164)
T ss_dssp             CSS
T ss_pred             ecC
Confidence            997

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.46  E-value=2.4e-13  Score=120.36  Aligned_cols=73  Identities=19%  Similarity=0.297  Sum_probs=66.8

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceE-EEEEecCHHHHHHHHHHhccCccCC--ceEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRF-AFIGYHREDQAQAALDYFNNTYVFS--SRIKV   90 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~-afv~f~~~~~a~~a~~~~~~~~~~~--~~i~v   90 (787)
                      +|+|.|     |||.+|+++|+++|+.||.|.+|.|+.+    ++|| |||.|.+.++|.+|++.|||..|.|  +.|+|
T Consensus        30 ~I~V~N-----L~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           30 RIIVEN-----LFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             EEEEES-----CCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             EEEECC-----CCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            355777     9999999999999999999999988764    3688 9999999999999999999999988  99999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      ++|++
T Consensus       101 ~~ak~  105 (130)
T 3zzy_A          101 DFSKL  105 (130)
T ss_dssp             EECSC
T ss_pred             EecCC
Confidence            99987

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=2e-13  Score=111.25  Aligned_cols=76  Identities=20%  Similarity=0.238  Sum_probs=66.8

Q ss_pred             CCCCcccce-EEEecCcccCCCccCCHHH----HHHHhhccC-ceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc
Q psy3345           6 SGPVVPRNH-ISLLDLDEVEFIYKITQEQ----LKAKFEEKG-TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN   79 (787)
Q Consensus         6 ~~~~~~~~~-~~~~~l~~~~lp~~~~~~~----l~~~f~~~g-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~   79 (787)
                      |+...|+.- |.|+|     ||+.+++++    |+++|+.|| .|.+|      .|   |+|||.|.+.++|++|++.||
T Consensus         2 ~~~~~p~~T~lYV~N-----L~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~   67 (96)
T 2diu_A            2 SSGSSGCHTLLYVYN-----LPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRME   67 (96)
T ss_dssp             CSSCCCSSEEEEEES-----CCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCCcceEEEEeC-----CCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhc
Confidence            344445665 77999     999999998    558999994 99999      23   999999999999999999999


Q ss_pred             cCccCCceEEEEEccC
Q psy3345          80 NTYVFSSRIKVEKCSN   95 (787)
Q Consensus        80 ~~~~~~~~i~v~~~~~   95 (787)
                      |..+.||.|+|.+|+.
T Consensus        68 G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A           68 NEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             TCCSSSSCCEEESSCC
T ss_pred             CCccCCceEEEEecCC
Confidence            9999999999999997

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.45  E-value=1.6e-13  Score=114.74  Aligned_cols=75  Identities=23%  Similarity=0.467  Sum_probs=69.6

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhcc----C-------ceEEEEEEecCCCCcceEEEEEecCHHHHHHHH
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEK----G-------TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL   75 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~   75 (787)
                      ||.-++.+|+|.|     ||+++|+++|+++|+.|    |       .|.+|.+..+     +|||||.|.+.++|.+|+
T Consensus         1 g~~~~~~~l~V~n-----Lp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~   70 (87)
T 2hzc_A            1 GPLGSARRLYVGN-----IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM   70 (87)
T ss_dssp             CCSGGGGEEEEES-----CCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG
T ss_pred             CCCCCCCEEEEeC-----CCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH
Confidence            5677889999999     99999999999999999    8       8999998765     799999999999999999


Q ss_pred             HHhccCccCCceEEEEE
Q psy3345          76 DYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        76 ~~~~~~~~~~~~i~v~~   92 (787)
                       .||+..|+||.|.|..
T Consensus        71 -~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           71 -AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             -GGTTCEETTEECEEEC
T ss_pred             -hcCCCEECCeEEEEeC
Confidence             9999999999999973

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.44  E-value=2.8e-13  Score=116.72  Aligned_cols=84  Identities=20%  Similarity=0.345  Sum_probs=72.4

Q ss_pred             CCCCEEEEecC--CccCc--------HHHHHHHHHhcCCeeEEEeccccCC-CCCCceEEEEEecCHHHHHHHHHHhcCC
Q psy3345         683 QTGSKILVRNI--PFQAK--------QSEVEELFKAFGELKFVRLPKKMVG-SGLHRGFGFVEFITKNEAKRAMKALCQS  751 (787)
Q Consensus       683 ~~~~~l~V~nL--p~~~t--------~~dL~~~F~~~G~I~~v~i~~~~~~-~g~~~g~afV~F~~~~~A~~Al~~l~~~  751 (787)
                      .|++.|.|+|+  |.++.        .+||++.|++||.|.+|+|+++... +++++|+|||+|.++++|.+|+..|| |
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~ln-G   81 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT-G   81 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHT-T
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhC-C
Confidence            47889999999  44443        4789999999999999999988521 24689999999999999999999997 7


Q ss_pred             eeecCceEEEEEcccc
Q psy3345         752 THLYGRRLVLEWAEEA  767 (787)
Q Consensus       752 ~~~~Gr~l~v~~A~~~  767 (787)
                      +.+.||.|+|+|+.++
T Consensus        82 ~~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           82 RKFANRVVVTKYCDPD   97 (105)
T ss_dssp             CEETTEECEEEEECHH
T ss_pred             CEeCCCEEEEEEeCHH
Confidence            9999999999999754

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.44  E-value=1.3e-13  Score=121.72  Aligned_cols=74  Identities=18%  Similarity=0.198  Sum_probs=67.3

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce---
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR---   87 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~---   87 (787)
                      ...+|+|.|     ||+++|++||+++|+.||.|.+|.|+.+      |||||+|.+.++|++||+.||+..|+|+.   
T Consensus        15 ~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~   83 (115)
T 3beg_B           15 SENRVVVSG-----LPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   83 (115)
T ss_dssp             --CCEEEEE-----CCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CCcEEEEeC-----CCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeee
Confidence            567899999     9999999999999999999999999875      89999999999999999999999999998   


Q ss_pred             --EEEEEccC
Q psy3345          88 --IKVEKCSN   95 (787)
Q Consensus        88 --i~v~~~~~   95 (787)
                        |.|..+.+
T Consensus        84 ~~i~v~~~~~   93 (115)
T 3beg_B           84 AYIRVKVDGP   93 (115)
T ss_dssp             CBCEEEECC-
T ss_pred             EEEEeccCCC
Confidence              88887775

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.44  E-value=4.8e-13  Score=129.44  Aligned_cols=123  Identities=15%  Similarity=0.235  Sum_probs=91.9

Q ss_pred             CHHHHHHHHHHh--CCCccCCeEEEEEecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCee
Q psy3345         636 TRESLNQALKVL--QNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK  713 (787)
Q Consensus       636 ~~e~A~~A~~~l--ng~~l~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~  713 (787)
                      +.+....|+...  ....+.+....|........+......     ......++|||+|||+.+|+++|+++|++||.|.
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~-----~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~  137 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEY-----KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVL  137 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHH-----HHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhh-----hhccccCEEEecCCCCcCCHHHHHHHHhcCCCEE
Confidence            567778888766  444555555555444211110000000     0112357899999999999999999999999999


Q ss_pred             EEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccc
Q psy3345         714 FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEA  767 (787)
Q Consensus       714 ~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~  767 (787)
                      +|+|+++.  +|.++|||||+|.+.++|.+|+..++  ..+.|++|.|.|+..-
T Consensus       138 ~v~i~~~~--~~~~kG~aFVeF~~~e~A~~A~~~~~--~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          138 NIQMRRTL--HKAFKGSIFVVFDSIESAKKFVETPG--QKYKETDLLILFKDDY  187 (193)
T ss_dssp             EEEEEECT--TCCEEEEEEEEESSHHHHHHHHHCTT--CEETTEECEEEETTTC
T ss_pred             EEEEEECC--CCCcccEEEEEECCHHHHHHHHHhCC--CeECCEEEEEEEhHHH
Confidence            99999984  69999999999999999999998774  5899999999998754

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=4.4e-13  Score=113.68  Aligned_cols=77  Identities=23%  Similarity=0.356  Sum_probs=69.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ...++|||+|||+++|+++|+++|+.||.|.+|  +.++.+|.   ||||+|.+.++|.+|++ |+|..+.|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345799999999999999999999999999987  55555555   99999999999999999 9999999999999988


Q ss_pred             CCC
Q psy3345         414 KPK  416 (787)
Q Consensus       414 ~~~  416 (787)
                      .++
T Consensus        80 ~~~   82 (94)
T 2e5g_A           80 EQK   82 (94)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            765

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=1.8e-13  Score=120.63  Aligned_cols=80  Identities=14%  Similarity=0.131  Sum_probs=69.9

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-C---CCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-E---GKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~---g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      ..-++.+|+|.|     ||+++|+++|+++|+.||.|. +.++.++ +   |+++|||||.|.+.++|++||+.|++  +
T Consensus         4 ~~~~~~~lfVgn-----Lp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~   75 (114)
T 2dnl_A            4 GSSGSRKVFVGG-----LPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--E   75 (114)
T ss_dssp             SSSCCCCEEEEC-----CCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--E
T ss_pred             CCCCCCEEEEcC-----CCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--c
Confidence            344578899999     999999999999999999999 8888876 3   79999999999999999999999854  7


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +|+.|.|..+.+
T Consensus        76 ~G~~~~~~~~~~   87 (114)
T 2dnl_A           76 DGKLYLCVSSPT   87 (114)
T ss_dssp             TTEEEEEECCSS
T ss_pred             CCcEEEeccCCC
Confidence            888888876654

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.43  E-value=2.2e-13  Score=117.43  Aligned_cols=81  Identities=12%  Similarity=0.231  Sum_probs=71.7

Q ss_pred             cccceEEEecCcccCC--CccC--------CHHHHHHHhhccCceEEEEEEecCCC---CcceEEEEEecCHHHHHHHHH
Q psy3345          10 VPRNHISLLDLDEVEF--IYKI--------TQEQLKAKFEEKGTVTDVQLKYTTEG---KFRRFAFIGYHREDQAQAALD   76 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~l--p~~~--------~~~~l~~~f~~~g~i~~~~~~~~~~g---~~~g~afv~f~~~~~a~~a~~   76 (787)
                      .|+..|+|+|     |  |..+        +++||++.|++||.|.+|+|+.++.+   +++|+|||.|.++++|.+|++
T Consensus         3 ~ps~vl~L~N-----m~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~   77 (105)
T 3v4m_A            3 HPTEVLCLMN-----MVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQ   77 (105)
T ss_dssp             SCCSEEEEES-----SCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHH
T ss_pred             CCCeEEEEEC-----CCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHH
Confidence            3678899999     5  4343        45799999999999999999998753   689999999999999999999


Q ss_pred             HhccCccCCceEEEEEccC
Q psy3345          77 YFNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        77 ~~~~~~~~~~~i~v~~~~~   95 (787)
                      .|||..++||.|.|.++.+
T Consensus        78 ~lnG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           78 GLTGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             HHTTCEETTEECEEEEECH
T ss_pred             HhCCCEeCCCEEEEEEeCH
Confidence            9999999999999999875

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=1.5e-13  Score=115.03  Aligned_cols=78  Identities=24%  Similarity=0.364  Sum_probs=67.7

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||.|||..+|+++|+++|++||.|.+|+|+++      ++|||||+|.+.++|++|+..   ...+.|++|.|.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------~~g~afV~f~~~~~a~~~~~~---~~~~~g~~l~v~   73 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQIAQSLCGE---DLIIKGISVHIS   73 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS------CCSCCEEECSCHHHHHHTTTC---EEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC------CCCEEEEEECCHHHHHHHhcC---CceeCCEEEEEE
Confidence            35789999999999999999999999999999999876      689999999999999865321   245689999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||.++..
T Consensus        74 ~a~~~~~   80 (88)
T 1wf0_A           74 NAEPKHN   80 (88)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9997764

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.41  E-value=3.4e-13  Score=118.92  Aligned_cols=76  Identities=16%  Similarity=0.382  Sum_probs=66.3

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce----
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR----  758 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~----  758 (787)
                      ...++|||.|||+.+|+++|+++|+.||.|.+|.|+.+        |||||+|.+.++|.+||..|| +..|.|++    
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--------g~afV~f~~~~~a~~Ai~~l~-g~~~~gr~~~~~   84 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVEFVRKEDMTYAVRKLD-NTKFRSHEGETA   84 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--------SEEEEEESSHHHHHHHHHHHT-TCBCCCTTSCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--------CEEEEEECCHHHHHHHHHHhC-CCEECCcEeeeE
Confidence            35689999999999999999999999999999999764        899999999999999999997 79999998    


Q ss_pred             -EEEEEcccc
Q psy3345         759 -LVLEWAEEA  767 (787)
Q Consensus       759 -l~v~~A~~~  767 (787)
                       |.|..+.+.
T Consensus        85 ~i~v~~~~~~   94 (115)
T 3beg_B           85 YIRVKVDGPR   94 (115)
T ss_dssp             BCEEEECC--
T ss_pred             EEEeccCCCC
Confidence             777777653

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.41  E-value=4.7e-13  Score=117.48  Aligned_cols=82  Identities=26%  Similarity=0.327  Sum_probs=71.8

Q ss_pred             CCCEEEEecC--CccC---cHHHHHHHHHhcCCeeEEEeccccC---CCCCCceEEEEEecCHHHHHHHHHHhcCCeeec
Q psy3345         684 TGSKILVRNI--PFQA---KQSEVEELFKAFGELKFVRLPKKMV---GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY  755 (787)
Q Consensus       684 ~~~~l~V~nL--p~~~---t~~dL~~~F~~~G~I~~v~i~~~~~---~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~  755 (787)
                      ++++|+|+|+  |.++   .++||++.|++||.|.+|+|+++..   .+++++|+|||+|.++++|.+|+..|| |+.+.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~Ln-Gr~f~   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN-GRWFA   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHT-TCEET
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHC-CCEEC
Confidence            6889999999  3333   3689999999999999999998852   246788999999999999999999997 79999


Q ss_pred             CceEEEEEccc
Q psy3345         756 GRRLVLEWAEE  766 (787)
Q Consensus       756 Gr~l~v~~A~~  766 (787)
                      ||.|+|+|+.+
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999975

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.41  E-value=4.5e-13  Score=129.68  Aligned_cols=78  Identities=15%  Similarity=0.232  Sum_probs=72.9

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      ...|+|.|     ||+++|+++|+++|+.||.|..|.|+++.+|+++|||||.|.+.++|.+|++.+ +..++||.|.|.
T Consensus       109 ~~~l~V~n-----Lp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~  182 (193)
T 2voo_A          109 NRSVYIKG-----FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLIL  182 (193)
T ss_dssp             HTEEEEEC-----CCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEE
T ss_pred             cCEEEecC-----CCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEE
Confidence            45699999     999999999999999999999999999989999999999999999999999875 569999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +++.
T Consensus       183 ~~~~  186 (193)
T 2voo_A          183 FKDD  186 (193)
T ss_dssp             ETTT
T ss_pred             EhHH
Confidence            8875

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.41  E-value=5.5e-13  Score=145.56  Aligned_cols=81  Identities=22%  Similarity=0.378  Sum_probs=77.2

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      .+...|+|.|     ||+.+|+++|+++|+.||.|..|.|+.++ +|+++|||||.|.+.++|.+||..||+..|.|+.|
T Consensus       100 ~~~~~lfV~n-----L~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i  174 (437)
T 3pgw_S          100 DAFKTLFVAR-----VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  174 (437)
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEE
Confidence            4557899999     99999999999999999999999999987 89999999999999999999999999999999999


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.+|.+
T Consensus       175 ~V~~a~~  181 (437)
T 3pgw_S          175 LVDVERG  181 (437)
T ss_pred             EEEEeCC
Confidence            9999986

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.40  E-value=5.4e-13  Score=111.42  Aligned_cols=72  Identities=26%  Similarity=0.503  Sum_probs=66.3

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhc----C-------CeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCC
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAF----G-------ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS  751 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~----G-------~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~  751 (787)
                      .+.++|||+|||..+|+++|+++|++|    |       .|.+++++++       +|||||+|.+.++|.+|+ .|| +
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-------kg~afV~f~~~~~a~~A~-~l~-g   74 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-------KNFAFLEFRSVDETTQAM-AFD-G   74 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-------SSEEEEEESSHHHHHHHG-GGT-T
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-------CcEEEEEcCCHHHHHHHH-hcC-C
Confidence            356899999999999999999999999    8       8999998765       799999999999999999 997 7


Q ss_pred             eeecCceEEEEE
Q psy3345         752 THLYGRRLVLEW  763 (787)
Q Consensus       752 ~~~~Gr~l~v~~  763 (787)
                      ..+.|++|+|+.
T Consensus        75 ~~~~g~~l~V~r   86 (87)
T 2hzc_A           75 IIFQGQSLKIRR   86 (87)
T ss_dssp             CEETTEECEEEC
T ss_pred             CEECCeEEEEeC
Confidence            999999999974

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=5.3e-13  Score=117.62  Aligned_cols=77  Identities=25%  Similarity=0.397  Sum_probs=66.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCC---CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET---DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~---~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      ...++|||+|||+++|+++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|.+|++.|+  .++|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4568999999999999999999999999999 888888776   7999999999999999999999884  366666666


Q ss_pred             eeC
Q psy3345         411 IPG  413 (787)
Q Consensus       411 ~~~  413 (787)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.38  E-value=8.8e-13  Score=130.03  Aligned_cols=80  Identities=24%  Similarity=0.451  Sum_probs=70.8

Q ss_pred             CCCCCEEEEecCCccC---------cHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCe
Q psy3345         682 KQTGSKILVRNIPFQA---------KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST  752 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~---------t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~  752 (787)
                      ....++|||+|||..+         ++++|+++|++||.|.+|+|+..       +|||||+|.+.++|..|+..|+ +.
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-------kG~AFV~F~~~~~Ae~A~~am~-g~  202 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-------KNCGFVKFKYQANAEFAKEAMS-NQ  202 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-------GTEEEEEESSHHHHHHHHHHHT-TC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-------CCEEEEEeCCHHHHHHHHHHhC-CC
Confidence            4567899999999998         79999999999999999999864       7999999999999999999997 68


Q ss_pred             ee------------cCceEEEEEcccccc
Q psy3345         753 HL------------YGRRLVLEWAEEADN  769 (787)
Q Consensus       753 ~~------------~Gr~l~v~~A~~~~~  769 (787)
                      .|            .|+.|.|.||.++.+
T Consensus       203 ~l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          203 TLLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EEeccccccccccCCCCEEEEEEccCCCC
Confidence            88            899999999997665

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.37  E-value=1.1e-12  Score=115.02  Aligned_cols=80  Identities=11%  Similarity=0.197  Sum_probs=70.8

Q ss_pred             ccceEEEecCcccCC--CccC---CHHHHHHHhhccCceEEEEEEecCC-----CCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345          11 PRNHISLLDLDEVEF--IYKI---TQEQLKAKFEEKGTVTDVQLKYTTE-----GKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus        11 ~~~~~~~~~l~~~~l--p~~~---~~~~l~~~f~~~g~i~~~~~~~~~~-----g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      |+..|+|+|     |  |-.+   .++||++.|++||.|.+|+|+.++.     |+++|+|||.|.++++|.+|++.|||
T Consensus        19 ps~vl~L~N-----m~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnG   93 (118)
T 3ue2_A           19 ESTVMVLRN-----MVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG   93 (118)
T ss_dssp             SCCEEEEES-----CSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCEEEEEC-----CCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCC
Confidence            678899999     5  3222   4799999999999999999999863     56889999999999999999999999


Q ss_pred             CccCCceEEEEEccC
Q psy3345          81 TYVFSSRIKVEKCSN   95 (787)
Q Consensus        81 ~~~~~~~i~v~~~~~   95 (787)
                      ..++||.|.|.++.+
T Consensus        94 r~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           94 RWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEECCcEEEEEEcCh
Confidence            999999999999875

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=4.9e-13  Score=111.88  Aligned_cols=75  Identities=19%  Similarity=0.302  Sum_probs=65.9

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .++.+|+|.|     ||+++|+++|+++|+.||.|.+|.|+.+    ++|||||.|.+.++|++|+..  ...+.|+.|.
T Consensus         3 ~~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~   71 (88)
T 1wf0_A            3 SGSSGVFVGR-----CTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVH   71 (88)
T ss_dssp             SCCCEEEEES-----CCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEE
T ss_pred             CCCcEEEEeC-----CCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEE
Confidence            4578899999     9999999999999999999999999864    789999999999999865432  3456999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.++.+
T Consensus        72 v~~a~~   77 (88)
T 1wf0_A           72 ISNAEP   77 (88)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999987

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=2.3e-12  Score=112.98  Aligned_cols=83  Identities=14%  Similarity=0.243  Sum_probs=70.5

Q ss_pred             cCCCCCEEEEecCCccC-----------cHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhc
Q psy3345         681 AKQTGSKILVRNIPFQA-----------KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC  749 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~-----------t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~  749 (787)
                      ...++++|+|+||....           ++++|+++|++||.|.+|.|+..     .++|||||+|.+.++|.+|+..||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~-----~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR-----HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT-----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecC-----CCCEEEEEEECCHHHHHHHHHHcC
Confidence            34578999999994332           26899999999999999977322     379999999999999999999997


Q ss_pred             CCeeecCceEEEEEcccccc
Q psy3345         750 QSTHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       750 ~~~~~~Gr~l~v~~A~~~~~  769 (787)
                       +..+.||+|.|+||.+..+
T Consensus        86 -g~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           86 -GRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             -TCEETTEECEEEECCSCCC
T ss_pred             -CCEECCcEEEEEEeCCCCC
Confidence             7999999999999988654

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.36  E-value=6.2e-13  Score=114.44  Aligned_cols=72  Identities=17%  Similarity=0.316  Sum_probs=64.0

Q ss_pred             EecCCccCcHHHHHHHH------------HhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         690 VRNIPFQAKQSEVEELF------------KAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       690 V~nLp~~~t~~dL~~~F------------~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      +.|||..+++++|++.|            ++||.|.+|+|+++.  .|+++|||||+|.++++|.+|+..|| |+.+.||
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~--~~~~~G~~fV~f~~~~~A~~A~~~ln-g~~~~Gr   96 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL--GDHLVGNVYVKFRREEDAEKAVIDLN-NRWFNGQ   96 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS--SSSSEEEEEEEESCHHHHHHHHHHHT-TCEETTE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC--CCCccEEEEEEECCHHHHHHHHHHHC-CCEECCE
Confidence            56777788887776666            999999999999884  68899999999999999999999997 7999999


Q ss_pred             eEEEEEc
Q psy3345         758 RLVLEWA  764 (787)
Q Consensus       758 ~l~v~~A  764 (787)
                      .|+|+|+
T Consensus        97 ~i~v~~s  103 (104)
T 1jmt_A           97 PIHAELS  103 (104)
T ss_dssp             ECCEEEC
T ss_pred             EEEEEEc
Confidence            9999997

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=3.6e-12  Score=111.77  Aligned_cols=79  Identities=9%  Similarity=0.235  Sum_probs=68.4

Q ss_pred             CcccceEEEecCcccCCCccC-----------CHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHH
Q psy3345           9 VVPRNHISLLDLDEVEFIYKI-----------TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDY   77 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~-----------~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~   77 (787)
                      +.++..|+|+|     |....           ++++|+++|++||.|.+|.| .++  .++|||||.|.+.++|.+|++.
T Consensus        12 ~~~s~~l~l~N-----l~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~   83 (112)
T 2dit_A           12 MRHERVVIIKN-----MFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQT   83 (112)
T ss_dssp             CCSCCEEEEES-----SCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHH
T ss_pred             CCCceEEEEEc-----CCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHH
Confidence            34677799999     73322           36899999999999999965 443  4899999999999999999999


Q ss_pred             hccCccCCceEEEEEccC
Q psy3345          78 FNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        78 ~~~~~~~~~~i~v~~~~~   95 (787)
                      ||+..|+||.|.|.++.+
T Consensus        84 lng~~~~gr~l~v~~a~~  101 (112)
T 2dit_A           84 LDGRWFGGRQITAQAWDG  101 (112)
T ss_dssp             STTCEETTEECEEEECCS
T ss_pred             cCCCEECCcEEEEEEeCC
Confidence            999999999999999987

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.31  E-value=1.8e-12  Score=112.92  Aligned_cols=87  Identities=8%  Similarity=0.070  Sum_probs=71.6

Q ss_pred             CCCCcccceEEEecCcccCC-----CccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345           6 SGPVVPRNHISLLDLDEVEF-----IYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~l-----p~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      +.|++|+..|.|+|+--..-     =+.-.++||++.|++||.|.+|.|..+   .++|+|||.|.+.++|.+|++.|||
T Consensus         1 ~~~p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~---~~~G~~fV~f~~~e~A~~Ai~~lnG   77 (114)
T 3s6e_A            1 GVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN---SAQGNVYVKCPSIAAAIAAVNALHG   77 (114)
T ss_dssp             -CCCCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT---CTTCCEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC---CCcEEEEEEECCHHHHHHHHHHhCC
Confidence            35788999999999211111     023346789999999999999999765   2599999999999999999999999


Q ss_pred             CccCCceEEEEEccC
Q psy3345          81 TYVFSSRIKVEKCSN   95 (787)
Q Consensus        81 ~~~~~~~i~v~~~~~   95 (787)
                      ..++||.|.|.++.+
T Consensus        78 ~~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           78 RWFAGKMITAAYVPL   92 (114)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEECCEEEEEEEEcH
Confidence            999999999999975

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=1.2e-11  Score=104.98  Aligned_cols=78  Identities=14%  Similarity=0.085  Sum_probs=63.4

Q ss_pred             cceEEEecCcccC--CCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          12 RNHISLLDLDEVE--FIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        12 ~~~~~~~~l~~~~--lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ..+|.|.-..-.+  -+..+|+++|+++|+.||.|.+|.|+    ++++|||||.|.+.++|..|++.+++  +.|+.|.
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEE
Confidence            4566666510000  12468999999999999999999998    57899999999999999999998554  6799999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.++++
T Consensus        84 V~~a~~   89 (100)
T 2d9o_A           84 ISWLEG   89 (100)
T ss_dssp             EECSSC
T ss_pred             EEEccC
Confidence            999986

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.28  E-value=5.2e-12  Score=124.55  Aligned_cols=76  Identities=9%  Similarity=0.172  Sum_probs=69.3

Q ss_pred             ccceEEEecCcccCCCccC---------CHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccC
Q psy3345          11 PRNHISLLDLDEVEFIYKI---------TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT   81 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~   81 (787)
                      +...|+|.|     ||+.+         ||++|+++|+.||.|.+|+|+.+     +|||||+|.+.++|+.|++.||+.
T Consensus       133 ~~rtLfVgn-----L~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~  202 (240)
T 3u1l_A          133 KNKTLYVGG-----IDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQ  202 (240)
T ss_dssp             CCCEEEEEC-----TTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCceeecCC-----CChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCC
Confidence            456788888     99998         89999999999999999999864     899999999999999999999999


Q ss_pred             cc------------CCceEEEEEccCC
Q psy3345          82 YV------------FSSRIKVEKCSNL   96 (787)
Q Consensus        82 ~~------------~~~~i~v~~~~~~   96 (787)
                      .|            .|+.|.|.+|++.
T Consensus       203 ~l~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          203 TLLLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CCCCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             EEeccccccccccCCCCEEEEEEccCC
Confidence            99            8999999999973

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.24  E-value=2.1e-11  Score=106.14  Aligned_cols=79  Identities=16%  Similarity=0.201  Sum_probs=68.0

Q ss_pred             CCCCEEEEecC--Ccc--------CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCe
Q psy3345         683 QTGSKILVRNI--PFQ--------AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST  752 (787)
Q Consensus       683 ~~~~~l~V~nL--p~~--------~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~  752 (787)
                      .++++|.|+|+  |.+        -.++||++.|++||.|.+|.|+++.     ++|+|||+|.+.++|.+|++.|| |+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~-----~~G~~fV~f~~~e~A~~Ai~~ln-G~   78 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS-----AQGNVYVKCPSIAAAIAAVNALH-GR   78 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC-----TTCCEEEECSSHHHHHHHHHHHT-TC
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC-----CcEEEEEEECCHHHHHHHHHHhC-CC
Confidence            46889999999  222        1246899999999999999997762     58999999999999999999997 79


Q ss_pred             eecCceEEEEEcccc
Q psy3345         753 HLYGRRLVLEWAEEA  767 (787)
Q Consensus       753 ~~~Gr~l~v~~A~~~  767 (787)
                      .+.||.|.|+|+.+.
T Consensus        79 ~f~GR~i~v~~~~~~   93 (114)
T 3s6e_A           79 WFAGKMITAAYVPLP   93 (114)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EECCEEEEEEEEcHH
Confidence            999999999999743

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=3.6e-11  Score=101.91  Aligned_cols=65  Identities=23%  Similarity=0.293  Sum_probs=58.2

Q ss_pred             ccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccccc
Q psy3345         695 FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD  768 (787)
Q Consensus       695 ~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~  768 (787)
                      ..+|+++|+++|++||.|.+|+|+.      +++|||||+|.+.++|..|+..++   .+.|++|+|+||++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~------~~rGfaFVeF~~~~~A~~Ai~~~~---~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSS------KKPGTAVVEFATVKAAELAVQNEV---GLVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEES------SSSSEEEEEESCHHHHHHHHHTCC---BCSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEcc------CCCCEEEEEECCHHHHHHHHHhcC---CCCCCeEEEEEccCCC
Confidence            5689999999999999999999974      379999999999999999999853   4689999999998665

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.13  E-value=1.2e-10  Score=121.25  Aligned_cols=77  Identities=19%  Similarity=0.384  Sum_probs=67.4

Q ss_pred             cCCCCCEEEEec--CCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeec---
Q psy3345         681 AKQTGSKILVRN--IPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY---  755 (787)
Q Consensus       681 ~~~~~~~l~V~n--Lp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~---  755 (787)
                      ...++.+|||.|  |++.+|+++|+++|++||.|.+|.++.       +||||||+|.+.++|++|++.|| |..+.   
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-------~kgfaFV~f~~~~~A~~Ai~~ln-G~~~~~~~   85 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-------NKPYSFARYRTTEESKRAYVTLN-GKEVVDDL   85 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-------TCSEEEEEESSHHHHHHHHHHTT-TCEEECTT
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-------CCCEEEEEECCHHHHHHHHHHhC-CCcccccc
Confidence            356889999999  588999999999999999999998854       37999999999999999999998 57663   


Q ss_pred             Cc--eEEEEEcc
Q psy3345         756 GR--RLVLEWAE  765 (787)
Q Consensus       756 Gr--~l~v~~A~  765 (787)
                      |+  .|.|.|++
T Consensus        86 g~~~~ly~~~~~   97 (345)
T 3tht_A           86 GQKITLYLNFVE   97 (345)
T ss_dssp             SCEEECEEEECS
T ss_pred             CCceEEEEEEee
Confidence            55  68999996

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.08  E-value=4.5e-10  Score=97.50  Aligned_cols=90  Identities=18%  Similarity=0.218  Sum_probs=79.0

Q ss_pred             cCCCCCEEEEecCCcc-CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecC-HHHHHHHHHHhc-CCeeecCc
Q psy3345         681 AKQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT-KNEAKRAMKALC-QSTHLYGR  757 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~-~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~-~~~A~~Al~~l~-~~~~~~Gr  757 (787)
                      ...+++.|+|.||+.. ++.++|+++|+.||.|.+|.+.++.       ..|||.|.+ +.+|..|+..|| ++..+.|.
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-------~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-------KEGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-------SEEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-------CEEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            3467899999999999 9999999999999999999998873       269999999 899999999995 36899999


Q ss_pred             eEEEEEccccccHHHHHHHH
Q psy3345         758 RLVLEWAEEADNVEDIRKRT  777 (787)
Q Consensus       758 ~l~v~~A~~~~~~~~~~~~~  777 (787)
                      .+.++....+++.+.|++..
T Consensus        87 ~~~~evL~GeeE~~yw~Ki~  106 (121)
T 1owx_A           87 EVTWEVLEGEVEKEALKKII  106 (121)
T ss_dssp             SEEEEECCHHHHHHHHHHHH
T ss_pred             EEEEEECCCHHHHHHHHHHH
Confidence            99999999888877776543

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.06  E-value=2e-10  Score=119.58  Aligned_cols=81  Identities=12%  Similarity=0.188  Sum_probs=67.8

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc--
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV--   83 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~--   83 (787)
                      ..+..|+.+|+|.|   .||++.+||++|+++|++||.|.+|.|..     +||||||+|.+.+||++|++.|||..+  
T Consensus        12 ~~~~~ps~~l~VgN---~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           12 ETVSYATQSLVVAN---GGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             CCCSSCCSEEEEET---CSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             eecCCCCCEEEEEc---CCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            34567889999987   44689999999999999999999987753     479999999999999999999999977  


Q ss_pred             -CCc--eEEEEEcc
Q psy3345          84 -FSS--RIKVEKCS   94 (787)
Q Consensus        84 -~~~--~i~v~~~~   94 (787)
                       .|+  .|.|.++.
T Consensus        84 ~~g~~~~ly~~~~~   97 (345)
T 3tht_A           84 DLGQKITLYLNFVE   97 (345)
T ss_dssp             TTSCEEECEEEECS
T ss_pred             ccCCceEEEEEEee
Confidence             356  45666664

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=8.9e-10  Score=89.03  Aligned_cols=75  Identities=20%  Similarity=0.352  Sum_probs=64.9

Q ss_pred             CCCCCEEEEecCCc----cCcH----HHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCee
Q psy3345         682 KQTGSKILVRNIPF----QAKQ----SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH  753 (787)
Q Consensus       682 ~~~~~~l~V~nLp~----~~t~----~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~  753 (787)
                      .+|..+|+|..+|.    ++-+    .+|.+.|+.||.|..+++..+.         +||+|.+.++|.+|++ || |..
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~---------~fVtF~d~~sAlaAi~-mn-G~~   72 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK---------MWVTFLEGSSALNVLS-LN-GKE   72 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS---------EEEEESSHHHHHHGGG-GT-TCE
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC---------EEEEECChHHHHHHHh-cC-CeE
Confidence            45778899988873    3333    6799999999999999998872         8999999999999999 97 799


Q ss_pred             ecCceEEEEEcccc
Q psy3345         754 LYGRRLVLEWAEEA  767 (787)
Q Consensus       754 ~~Gr~l~v~~A~~~  767 (787)
                      ++||.|+|++|.|+
T Consensus        73 v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           73 LLNRTITIALKSPS   86 (91)
T ss_dssp             ETTEEEEEEECCCS
T ss_pred             eCCeEEEEEeCCCC
Confidence            99999999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.92  E-value=3.8e-09  Score=91.63  Aligned_cols=83  Identities=13%  Similarity=0.078  Sum_probs=73.0

Q ss_pred             CCCCCCCCcccceEEEecCcccCCCcc-CCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecC-HHHHHHHHHHhc
Q psy3345           2 FNHLSGPVVPRNHISLLDLDEVEFIYK-ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHR-EDQAQAALDYFN   79 (787)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~l~~~~lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~-~~~a~~a~~~~~   79 (787)
                      ++|.|.+-++..-|.|.|     ||+. +|+++|+++|+.||.|..|.|+.+.     -.|||.|.+ +++|..|++.+|
T Consensus         8 ~~~~~~~~~~G~il~v~~-----l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln   77 (121)
T 1owx_A            8 HHHGSLEEKIGCLLKFSG-----DLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDAN   77 (121)
T ss_dssp             -CCCCCSCCCCCEEEEEE-----SCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTT
T ss_pred             cccCcccccCCeEEEEec-----CCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhh
Confidence            466777777888889999     9999 9999999999999999999998873     269999999 799999999995


Q ss_pred             --cCccCCceEEEEEcc
Q psy3345          80 --NTYVFSSRIKVEKCS   94 (787)
Q Consensus        80 --~~~~~~~~i~v~~~~   94 (787)
                        +..|+|..+.++...
T Consensus        78 ~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           78 NGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             TSCBCTTSSSEEEEECC
T ss_pred             cCCcEEeCcEEEEEECC
Confidence              779999999998775

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.83  E-value=8.5e-09  Score=102.42  Aligned_cols=90  Identities=11%  Similarity=0.189  Sum_probs=75.6

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCC-----CCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-----GKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~-----g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      .+...++..+.+.++-.......-.++||++.|++||.|.+|.|+.+..     |+++|++||.|.+.++|.+|++.|||
T Consensus       118 ~~~~~~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~g  197 (222)
T 3dxb_A          118 AGSAMESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG  197 (222)
T ss_dssp             CCSCCBCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             cccccccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcC
Confidence            3445556667777755445555667889999999999999999997653     38999999999999999999999999


Q ss_pred             CccCCceEEEEEccC
Q psy3345          81 TYVFSSRIKVEKCSN   95 (787)
Q Consensus        81 ~~~~~~~i~v~~~~~   95 (787)
                      ..++||.|.|.++..
T Consensus       198 r~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          198 RWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             CBSSSSBCEEEECCH
T ss_pred             ceECCeEEEEEEcCH
Confidence            999999999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.81  E-value=1.1e-08  Score=82.76  Aligned_cols=72  Identities=13%  Similarity=0.162  Sum_probs=61.0

Q ss_pred             ccceEEEecCcccCCC----ccCCH----HHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCc
Q psy3345          11 PRNHISLLDLDEVEFI----YKITQ----EQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY   82 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp----~~~~~----~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~   82 (787)
                      |...|.|..     +|    .+.-.    .+|.+.|+.||.|..|+|+.++       +||+|.+.++|.+||+ |||..
T Consensus         6 pd~tv~V~~-----~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~   72 (91)
T 2dnr_A            6 SGGTVLVSI-----KSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKE   72 (91)
T ss_dssp             SSCEEEEEE-----ECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCE
T ss_pred             CCCeEEEEe-----ccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeE
Confidence            345566666     55    23333    6799999999999999999873       8999999999999999 89999


Q ss_pred             cCCceEEEEEccC
Q psy3345          83 VFSSRIKVEKCSN   95 (787)
Q Consensus        83 ~~~~~i~v~~~~~   95 (787)
                      +.||.|+|..+++
T Consensus        73 v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           73 LLNRTITIALKSP   85 (91)
T ss_dssp             ETTEEEEEEECCC
T ss_pred             eCCeEEEEEeCCC
Confidence            9999999999986

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.69  E-value=2.8e-08  Score=80.64  Aligned_cols=75  Identities=13%  Similarity=0.219  Sum_probs=64.3

Q ss_pred             cCCCCCEEEEecCCcc-----CcH----HHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCC
Q psy3345         681 AKQTGSKILVRNIPFQ-----AKQ----SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS  751 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~-----~t~----~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~  751 (787)
                      ..+|..+|+|..++..     +-+    .+|.+.|+.||.|..+++..+.         +||+|.+.++|.+||. || |
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---------~fVtF~d~~sAl~AI~-ld-G   79 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---------MLVTFADSHSALSVLD-VD-G   79 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---------EEEECSCSHHHHHHHH-GG-G
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---------EEEEEcChHHHHHHHh-cC-C
Confidence            3568889999998743     322    5699999999999999998882         9999999999999998 97 7


Q ss_pred             eeecCceEEEEEccc
Q psy3345         752 THLYGRRLVLEWAEE  766 (787)
Q Consensus       752 ~~~~Gr~l~v~~A~~  766 (787)
                      ..++||.|+|++..+
T Consensus        80 ~~v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           80 MKVKGRAVKISGPSS   94 (95)
T ss_dssp             SEETTEEEEEECCCC
T ss_pred             eeeCCeEEEEeccCC
Confidence            999999999998654

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.69  E-value=3.9e-08  Score=97.59  Aligned_cols=70  Identities=26%  Similarity=0.277  Sum_probs=61.8

Q ss_pred             CcHHHHHHHHHhcCCeeEEEecccc---CCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccc
Q psy3345         697 AKQSEVEELFKAFGELKFVRLPKKM---VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEA  767 (787)
Q Consensus       697 ~t~~dL~~~F~~~G~I~~v~i~~~~---~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~  767 (787)
                      -.+++|++.|++||.|.++.|+++.   ..+|+++|++||+|.+.++|.+|++.|| |+.+.||.|.++|+..+
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~-gr~~~gr~i~~~~~~~~  213 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN-GRWFAGRKVVAEVYDQE  213 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHT-TCBSSSSBCEEEECCHH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhc-CceECCeEEEEEEcCHH
Confidence            3568899999999999999998664   1345899999999999999999999997 79999999999998743

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.59  E-value=9e-08  Score=77.66  Aligned_cols=71  Identities=13%  Similarity=0.099  Sum_probs=60.4

Q ss_pred             cccceEEEecCcccCCCcc-----CCH----HHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhcc
Q psy3345          10 VPRNHISLLDLDEVEFIYK-----ITQ----EQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN   80 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~-----~~~----~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~   80 (787)
                      .|...|.|..     ++.+     .-.    .+|.+.|+.||+|..|+|+.++       +||+|.+.++|.+||+ |||
T Consensus        13 PpD~Tv~V~~-----~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG   79 (95)
T 1ufw_A           13 PLDATVVVNL-----QSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDG   79 (95)
T ss_dssp             CTTCEEEEEE-----SSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGG
T ss_pred             CCCCeEEEEe-----cCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCC
Confidence            4566788888     7632     222    5689999999999999999883       9999999999999999 899


Q ss_pred             CccCCceEEEEEc
Q psy3345          81 TYVFSSRIKVEKC   93 (787)
Q Consensus        81 ~~~~~~~i~v~~~   93 (787)
                      ..+.||.|.|..-
T Consensus        80 ~~v~Gr~L~V~~k   92 (95)
T 1ufw_A           80 MKVKGRAVKISGP   92 (95)
T ss_dssp             SEETTEEEEEECC
T ss_pred             eeeCCeEEEEecc
Confidence            9999999999754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.28  E-value=3e-06  Score=69.86  Aligned_cols=73  Identities=12%  Similarity=0.099  Sum_probs=69.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHhhccC-----CCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEe
Q psy3345         446 SKRIILVKNLPYRTLPTDLKALFEPF-----GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  518 (787)
Q Consensus       446 ~~~~i~v~nlp~~~t~~~l~~~F~~~-----G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~  518 (787)
                      ..++|-+-|||..+++..|+.+..++     |.+..+.+.++.+-|+|+|.+...|.+|.-.|+|..|.|++|.+.-.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            46889999999999999999999999     99999999999999999999999999999999999999999998744

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.25  E-value=1e-05  Score=66.76  Aligned_cols=86  Identities=10%  Similarity=0.138  Sum_probs=73.9

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhc-----CCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAF-----GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~-----G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      ...++|-+.|||..+++..|+.+..+|     |.|..+.+..+.       |-|+|+|.+...|-+|...|+ |..|.||
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-------~GAivef~d~~~AgKasLaL~-G~ef~gr   90 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-------NGAIIIFRDSKFAAKMLMILN-GSQFQGK   90 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-------TEEEEECSCHHHHHHHHHHHS-SEEETTE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-------CceEEEEccchhhHHHHhhcC-CeeecCe
Confidence            347889999999999999999999999     999999998883       449999999999999999997 7999999


Q ss_pred             eEEEEEccccccHHHHHHHHhhhcc
Q psy3345         758 RLVLEWAEEADNVEDIRKRTNRYFG  782 (787)
Q Consensus       758 ~l~v~~A~~~~~~~~~~~~~~~~~~  782 (787)
                      +|++.-      +.+|++-.+++++
T Consensus        91 ~Lr~gT------v~eL~~~~~~~~~  109 (117)
T 2l9w_A           91 VIRSGT------INDMKRYYNNQQN  109 (117)
T ss_dssp             EEEEEC------HHHHHHHHHHHHC
T ss_pred             EEEecC------HHHHHhccccccc
Confidence            999864      4466655555543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.98  E-value=3.3e-05  Score=63.46  Aligned_cols=70  Identities=19%  Similarity=0.226  Sum_probs=59.5

Q ss_pred             CccceEEEeCCCCCCCHHhHHHhhcCC-----CCc-ceeecccceEEEeecChHhHHHHHhcCCcccCCeeEEEeec
Q psy3345         222 RQYHTIVVKNLPAGVKKKDLKAYFKPL-----PLA-SVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKY  292 (787)
Q Consensus       222 ~~~~~v~v~nLp~~~te~di~~~F~~~-----g~v-~i~i~~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~  292 (787)
                      ....+|.|.|||..+.++.|.-+|..-     |.+ .+.... +-|+|+|.+.+.|++.|+.....|.+..|.|.++
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P~   81 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-CGGVLTFREPADAERVLAQADHELHGAQLSLRPA   81 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEEEC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-CcEEEEEcChHHHHHHhcCCcceecCeEEEEEcC
Confidence            456899999999999999999999872     455 555556 8999999999999999998788899999999753

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.71  E-value=0.00027  Score=58.08  Aligned_cols=88  Identities=26%  Similarity=0.304  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc-----CCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKY-----GPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH  409 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~-----G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~  409 (787)
                      ...+|.|.|||..+.++.|.-+|+.-     |+|..+....        +-|+|+|.+.+.|++.++ .....|+|..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEE
Confidence            45689999999999999999999862     6888887643        369999999999999996 346789999999


Q ss_pred             EeeCCCCCCCCCCCCCccccccccccchhhhhhhcCCCCEEEEeCCCCCCC
Q psy3345         410 LIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTL  460 (787)
Q Consensus       410 v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~t  460 (787)
                      |.+..+.                             ...++++++||..++
T Consensus        78 V~P~~~~-----------------------------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           78 LRPAPPR-----------------------------APARLLLQGLPPGTS   99 (104)
T ss_dssp             EEECCCC-----------------------------CCCCCCCCSCCCCCC
T ss_pred             EEcCCCC-----------------------------CcceEeeecCCCCCC
Confidence            9887654                             346688888887764

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.43  E-value=0.00032  Score=58.02  Aligned_cols=76  Identities=17%  Similarity=0.214  Sum_probs=64.7

Q ss_pred             CCEEEEecCCccC-c----HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         685 GSKILVRNIPFQA-K----QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       685 ~~~l~V~nLp~~~-t----~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      .++|+|.||+.++ +    .+.++++|..|+.+......+.+      | =..|.|.++++|.+|-..|+ ++.++|++|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------R-Rirv~F~~~~~A~~AR~~Lh-~~~f~g~~~   76 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------K-RVRINFSNPLSAADARLRLH-KTEFLGKEM   76 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------T-EEEEECSSTTHHHHHHHTST-TSEETTEEC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------e-EEEEEeCChHHHHHHHHHhc-cceecCcee
Confidence            4689999998876 2    25689999999999888877764      2 26899999999999999996 799999999


Q ss_pred             EEEEccccc
Q psy3345         760 VLEWAEEAD  768 (787)
Q Consensus       760 ~v~~A~~~~  768 (787)
                      +|-||++.+
T Consensus        77 r~YFgq~~~   85 (104)
T 1wey_A           77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEEecCCCC
Confidence            999998554

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.26  E-value=0.00076  Score=55.75  Aligned_cols=73  Identities=14%  Similarity=0.010  Sum_probs=65.6

Q ss_pred             CCEEEEeCCCCCC-C----HHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEec
Q psy3345         447 KRIILVKNLPYRT-L----PTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  519 (787)
Q Consensus       447 ~~~i~v~nlp~~~-t----~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  519 (787)
                      .++|+|.||+.++ .    .+.++++|..|+++......++=.-..|.|.++++|.+|-..|++..+.|..++|-++.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            4789999998765 2    25778999999999998888888889999999999999999999999999999999986

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.24  E-value=0.0011  Score=53.96  Aligned_cols=67  Identities=12%  Similarity=0.164  Sum_probs=55.8

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC---CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT---EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~---~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      .+|.||.     ||+++||+++.+.++.+..+.-..++..+   .-....-|||.|.+.+++..-.+.+||..|.
T Consensus         2 ~KvVIRr-----LPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRR-----LPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEE-----ECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeC-----CCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4789999     99999999999999999877666665543   1234578999999999999999999998653

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.15  E-value=0.0014  Score=55.83  Aligned_cols=77  Identities=17%  Similarity=0.233  Sum_probs=62.4

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      +.......-|.|-|     .|... -..|..+|+.||.|.+....     ....+-.|+|.+..+|++||.+ ||..|.|
T Consensus        18 ~~~~~~~~wVtVFG-----Fp~~~-~~~VL~~F~~~G~Iv~~~~~-----~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g   85 (119)
T 1wwh_A           18 SEDHLDDTWVTVFG-----FPQAS-ASYILLQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALSK-DGRIFGE   85 (119)
T ss_dssp             ---CGGGGEEEEEC-----CCGGG-HHHHHHHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHTT-TTCEETT
T ss_pred             CCCCCCCCEEEEEC-----CCHHH-HHHHHHHHHhhCcEEEeccC-----CCCCeEEEEeCCHHHHHHHHHh-CCeEecC
Confidence            34455567788888     99886 67788999999999988762     2357999999999999999999 9999985


Q ss_pred             -ceEEEEEcc
Q psy3345          86 -SRIKVEKCS   94 (787)
Q Consensus        86 -~~i~v~~~~   94 (787)
                       -.|-|.++.
T Consensus        86 ~~mIGV~p~~   95 (119)
T 1wwh_A           86 SIMIGVKPCI   95 (119)
T ss_dssp             TEECEEEECC
T ss_pred             CEEEEEEECC
Confidence             678898875

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.01  E-value=0.0019  Score=52.29  Aligned_cols=54  Identities=19%  Similarity=0.259  Sum_probs=49.8

Q ss_pred             CccceEEEeCCCCCCCHHhHHHhhcCCCCcceeecccceEEEeecChHhHHHHHh
Q psy3345         222 RQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALN  276 (787)
Q Consensus       222 ~~~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~~~g~afV~F~~~~~A~~Al~  276 (787)
                      .-.++++| +.|......||.++|++||-+.|+.+....|||.|.+++.|..|+.
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCEEEEEEcCCeEEEEecCHHHHHHHHH
Confidence            34578888 9999999999999999999888888888999999999999999998

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.83  E-value=0.0046  Score=50.30  Aligned_cols=68  Identities=19%  Similarity=0.225  Sum_probs=55.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCC--cceEEEEEEcCHHHHHHHHHHhCCceeC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK--TKGFALVTFLMPEHATQAYQHLDGTVFL  404 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~--~~g~afV~F~~~~~A~~a~~~l~~~~~~  404 (787)
                      .+|.|++||+.+|++++.+.++....+.....+..+.+..  .-.-|||.|.+.+++..-.+.++|..+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4799999999999999999999988776666655443322  3356999999999999999999998774

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.63  E-value=0.0066  Score=49.18  Aligned_cols=62  Identities=18%  Similarity=0.218  Sum_probs=51.4

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN   79 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~   79 (787)
                      ..|...+.+|++.+     +|......||.++|+.||. ..|+-+-|      .-|||.|.+++.|..|++.+.
T Consensus         9 ~d~~p~r~HVf~l~-----FP~ewKt~DI~~lFs~fgg-v~I~WidD------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A            9 PDLQPKRDHVLHVT-----FPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SCCCCCCCSEEEEE-----CCTTCCHHHHHHHHTTTCS-CCCEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCeEEEEe-----CChhhhhHHHHHHhhccCC-EEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            45666788888889     9999999999999999984 34555544      489999999999999999753

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.60  E-value=0.0016  Score=53.00  Aligned_cols=52  Identities=19%  Similarity=0.243  Sum_probs=48.2

Q ss_pred             cceEEEeCCCCCCCHHhHHHhhcCCCCcceeecccceEEEeecChHhHHHHHh
Q psy3345         224 YHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALN  276 (787)
Q Consensus       224 ~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~~~g~afV~F~~~~~A~~Al~  276 (787)
                      .++++| +.|......||.++|++||-+.|+.+....|||.|.+++.|..|+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCEEEEEEcCCeEEEEecCHHHHHHHHH
Confidence            467778 9999999999999999999778888888999999999999999998

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.43  E-value=0.0083  Score=51.12  Aligned_cols=72  Identities=15%  Similarity=0.184  Sum_probs=60.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC-eeEEEEEe
Q psy3345         445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE-VPLYLEWA  518 (787)
Q Consensus       445 ~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g-~~l~v~~~  518 (787)
                      ...+-|.|-+.|... ...|...|+.||.|.+...+..+....|+|.++.+|++|+. .||..+.| ..|-|.+.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            346789999999874 67889999999999998887788899999999999999998 59999874 55666654

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.36  E-value=0.0022  Score=55.37  Aligned_cols=77  Identities=18%  Similarity=0.144  Sum_probs=58.0

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEE-EEEEec------------C-CC-CcceEEEEEecCHHHHHHHHH
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD-VQLKYT------------T-EG-KFRRFAFIGYHREDQAQAALD   76 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~-~~~~~~------------~-~g-~~~g~afv~f~~~~~a~~a~~   76 (787)
                      .+-|.|-|     .|.+.+ ..+-++|+.||.|.+ +.....            + -+ ....+..|+|.++.+|.+||.
T Consensus         7 e~~VtVFG-----Fp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~   80 (132)
T 3p3d_A            7 ELAILVFG-----YPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL   80 (132)
T ss_dssp             -CEEEEEC-----CCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT
T ss_pred             ceEEEEEe-----cCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH
Confidence            45577888     886554 567789999998755 322210            0 00 135788999999999999999


Q ss_pred             HhccCccCCceEEEEEccC
Q psy3345          77 YFNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        77 ~~~~~~~~~~~i~v~~~~~   95 (787)
                      + ||..|.|..|-|.++++
T Consensus        81 ~-NG~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           81 E-NGAVFNGVLLGVIPYTK   98 (132)
T ss_dssp             T-TTCEETTEECEEEECCH
T ss_pred             h-CCeEeCcEEEEEEECCH
Confidence            9 99999999999999975

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.05  E-value=0.01  Score=48.32  Aligned_cols=58  Identities=16%  Similarity=0.232  Sum_probs=47.3

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN   79 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~   79 (787)
                      .++.+|+..+     +|......||.++|+.||. ..|.-+-|      .-|||.|.+++.|..|++.+.
T Consensus         3 ~~R~HV~~l~-----FP~ewKt~Di~~lFs~fgg-v~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            3 LGSDHVLHVT-----FPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             SEEEEEEEEE-----CCTTCCHHHHHHHTTTSEE-EEEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             CCCCeEEEEe-----CChhhhhHHHHHHHhccCC-EEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            4566777778     9999999999999999983 33444444      489999999999999999753

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.86  E-value=0.0064  Score=49.67  Aligned_cols=69  Identities=13%  Similarity=0.142  Sum_probs=50.4

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC---CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT---EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~---~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      -+-+|.||.     ||+++||+++.+.++.+=.++-..++.-+   ......-|||.|.+.+|.....+.++|..|.
T Consensus         8 ~~~KvVIRr-----LPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            8 HSHMVVIRR-----LPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCCEEEEC-----CCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             cceeEEEeC-----CCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            357899999     99999999998888876443222221111   1113367999999999999999999998653

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.77  E-value=0.013  Score=50.65  Aligned_cols=92  Identities=20%  Similarity=0.147  Sum_probs=60.9

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeE-EEeccccC-----------CCC-CCceEEEEEecCHHHHHHHHHHhcC
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMV-----------GSG-LHRGFGFVEFITKNEAKRAMKALCQ  750 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~-v~i~~~~~-----------~~g-~~~g~afV~F~~~~~A~~Al~~l~~  750 (787)
                      ..+.|.|.+.|...+.. |.+.|++||.|.. +.+.+...           -.+ ....+..|.|.++.+|.+||+.  |
T Consensus         6 ~e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~--N   82 (132)
T 3p3d_A            6 GELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE--N   82 (132)
T ss_dssp             --CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT--T
T ss_pred             CceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh--C
Confidence            35679999997776655 7779999999865 22222100           001 1245789999999999999997  5


Q ss_pred             CeeecCceEEEEEccccccHHHHHHHHhh
Q psy3345         751 STHLYGRRLVLEWAEEADNVEDIRKRTNR  779 (787)
Q Consensus       751 ~~~~~Gr~l~v~~A~~~~~~~~~~~~~~~  779 (787)
                      |..+.|.-|=|.... +..++.|.++...
T Consensus        83 G~ii~G~mIGV~Py~-~~~ve~l~~~~~~  110 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYT-KDAVERLQKRKLT  110 (132)
T ss_dssp             TCEETTEECEEEECC-HHHHHHHC-----
T ss_pred             CeEeCcEEEEEEECC-HHHHHHHhcCCcc
Confidence            899999988888885 4455555444333

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.32  E-value=0.041  Score=44.94  Aligned_cols=73  Identities=14%  Similarity=0.224  Sum_probs=55.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCC--------cEEEEEeCCHHHHHHHHHHhcCCeeCC-----eeE
Q psy3345         447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG--------ITGLVEFLQKNQAKAAFNSLAYTKFKE-----VPL  513 (787)
Q Consensus       447 ~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--------~~a~V~F~~~~~A~~A~~~l~~~~~~g-----~~l  513 (787)
                      +-.|.|+.||+.+|++++.+.++.+-.+......+.+        .-|||.|.+.++...-...++|..|.+     -+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            4579999999999999999888876555433333211        249999999999999999999988763     344


Q ss_pred             EEEEec
Q psy3345         514 YLEWAP  519 (787)
Q Consensus       514 ~v~~~~  519 (787)
                      .|++||
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            566665

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.95  E-value=0.054  Score=58.27  Aligned_cols=57  Identities=19%  Similarity=0.264  Sum_probs=44.0

Q ss_pred             cCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCc-EEEEEeCCHHHHHHHHH
Q psy3345         444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFN  501 (787)
Q Consensus       444 ~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~-~a~V~F~~~~~A~~A~~  501 (787)
                      ....+.|+|. +|..+++.+|.+.|++||.|.++.+..++| +|+|+|.+.+++..++.
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            3346789998 799999999999999999999999988665 89999999999987754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.06  E-value=0.082  Score=56.85  Aligned_cols=57  Identities=14%  Similarity=0.251  Sum_probs=43.4

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHH
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA  747 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~  747 (787)
                      ..+.|+|. .|..+++.+|.++|++||.|.++.+.++.      .-||.|+|.+.+++..++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~------g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF------GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS------SEEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC------CeEEEEEeCCHHHHHHHHhc
Confidence            34679997 79999999999999999999999887762      36999999999999977654

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=81.45  E-value=2.6  Score=46.27  Aligned_cols=52  Identities=19%  Similarity=0.240  Sum_probs=47.2

Q ss_pred             cceEEEeCCCCCCCHHhHHHhhcCCCCcceeecccceEEEeecChHhHHHHHh
Q psy3345         224 YHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALN  276 (787)
Q Consensus       224 ~~~v~v~nLp~~~te~di~~~F~~~g~v~i~i~~~g~afV~F~~~~~A~~Al~  276 (787)
                      +++++|+ +|..+...+|.+.|+.+|.+.|+.+....|||.|.+.+.|..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~V~widdt~a~V~~~~~~~a~~~l~  491 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVN  491 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCEEEECSSSEEEEECSCHHHHHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEEEEEEcCCeEEEEECCHHHHHHHHH
Confidence            4577776 999999999999999999889988888899999999999999988

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=81.08  E-value=3  Score=45.72  Aligned_cols=61  Identities=18%  Similarity=0.219  Sum_probs=49.9

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN   79 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~   79 (787)
                      .|.+.+.++++.+     +|......||.++|+.||. .+|+-+-+      ..|||.|.++++|..+++.+.
T Consensus       434 d~~~~R~~vl~v~-----f~~~~~~~~i~~~fs~fg~-v~V~widd------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          434 DLQPKRDHVLHVT-----FPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             CCCCCGGGEEEEE-----CCTTCCHHHHHHHGGGGCC-CEEEECSS------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CCCCCcCcEEEEe-----CCCCCCHHHHHHHHHhcCC-EEEEEEcC------CeEEEEECCHHHHHHHHHHHH
Confidence            3445677888888     9999999999999999995 45554433      469999999999999999975

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	787
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-05
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-04
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-19
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-14
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-16
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-06
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-15
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.003
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-04
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-15
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	0.003
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-14
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.002
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-14
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	0.004
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	0.002
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-04
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-04
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-10
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-13
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	0.003
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-04
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-05
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-04
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-12
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	0.001
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-07
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-12
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	7e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	9e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	0.003
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.001
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	9e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	6e-11
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.004
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.002
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.001
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 5e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 4e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 5e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	7e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.002
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	0.003
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	0.002
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	9e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	7e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.002
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	4e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.001
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	7e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.003
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	9e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	9e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	7e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	7e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	5e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.001
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.002
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.004

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 88.1 bits (218), Expect = 1e-21
 Identities = 66/90 (73%), Positives = 73/90 (81%)

Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
           KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 742 KRAMKALCQSTHLYGRRLVLEWAEEADNVE 771
           K+A  ALC STHLYGRRLVLEWA+    V+
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.8 bits (168), Expect = 6e-15
 Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKE-TDKTKGFALVTFLMPEHATQ 393
            + +I VRN+ +   + ++ +LF  +G L  V LP     T   +GF  V F+  + A +
Sbjct: 7   TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 66

Query: 394 AYQHL-DGTVFLGRMLHLIPGKPKE 417
           A+  L   T   GR L L     + 
Sbjct: 67  AFNALCHSTHLYGRRLVLEWADSEV 91

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.7 bits (160), Expect = 7e-14
 Identities = 19/95 (20%), Positives = 45/95 (47%), Gaps = 5/95 (5%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           + +  + + ++N+ F + +  IR  F   G + +V + +K            G+GFV F 
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGA----HRGFGFVDFI 59

Query: 636 TRESLNQALKVLQNSS-LDEHQIELKRSNRNLESE 669
           T++   +A   L +S+ L   ++ L+ ++  +  +
Sbjct: 60  TKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 8/87 (9%)

Query: 440 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQ 492
           QV + ++   ILV+N+P++    +++ LF  FG+L  V +P        +   G V+F+ 
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 493 KNQAKAAFNSLAY-TKFKEVPLYLEWA 518
           K  AK AFN+L + T      L LEWA
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEWA 87

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
          ++  Q +++  F   G +  V+L  K T  G  R F F+ +  +  A+ A +   ++   
Sbjct: 18 FQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL 77

Query: 85 SSR-IKVEKCSN 95
            R + +E   +
Sbjct: 78 YGRRLVLEWADS 89

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 12/90 (13%)

Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKP--------LPLASVRT-TFLGMAYIGFKDEKNC 271
           K+    I+V+N+P    +++++  F          LP     T    G  ++ F  +++ 
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 272 NKALNK--NKSFWKGKQLNIYKYSKDNSAK 299
            KA N   + +   G++L + +++      
Sbjct: 65  KKAFNALCHSTHLYGRRLVL-EWADSEVTV 93

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.7 bits (203), Expect = 9e-19
 Identities = 46/191 (24%), Positives = 84/191 (43%), Gaps = 17/191 (8%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +EPE    L+I  L+F +T++S+R HF++ G +    V R  + K        G+GFV +
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRS-----RGFGFVTY 55

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP 694
            T E ++ A+   +   +D   +E KR+           +      A  T  KI V  I 
Sbjct: 56  ATVEEVDAAMN-ARPHKVDGRVVEPKRAVSR--------EDSQRPGAHLTVKKIFVGGIK 106

Query: 695 FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL 754
              ++  + + F+ +G+++ + +     GSG  RGF FV F   +   + +    +   +
Sbjct: 107 EDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDSVDKIVIQ--KYHTV 163

Query: 755 YGRRLVLEWAE 765
            G    +  A 
Sbjct: 164 NGHNCEVRKAL 174

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.0 bits (170), Expect = 2e-14
 Identities = 32/202 (15%), Positives = 62/202 (30%), Gaps = 25/202 (12%)

Query: 216 KAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKAL 275
           K P   R    + +  L      + L+++F+                  +    +C    
Sbjct: 1   KEPEQLR---KLFIGGLSFETTDESLRSHFEQ-----------------WGTLTDCVVMR 40

Query: 276 NKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAE 335
           + N    +G     Y   ++  A    A +   +     +         +  Q       
Sbjct: 41  DPNTKRSRGFGFVTYATVEEVDA----AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLT 96

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
             +IFV  +     E  L   FE+YG +  + +  D+ + K +GFA VTF   +   +  
Sbjct: 97  VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156

Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
                    G    +     K+
Sbjct: 157 I-QKYHTVNGHNCEVRKALSKQ 177

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (137), Expect = 5e-10
 Identities = 33/187 (17%), Positives = 62/187 (33%), Gaps = 27/187 (14%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++F+  LS+  T++ L   FE++G L + ++  D  T +++GF  VT+   E    A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 65

Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
                                   VDG+V         +   +     + + I V  +  
Sbjct: 66  ------------------NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 107

Query: 458 RTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSLAYTKFKEV 511
            T    L+  FE +G +  + +     +G       V F   +          Y      
Sbjct: 108 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGH 166

Query: 512 PLYLEWA 518
              +  A
Sbjct: 167 NCEVRKA 173

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (122), Expect = 4e-08
 Identities = 27/230 (11%), Positives = 67/230 (29%), Gaps = 48/230 (20%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 502
           E    R + +  L + T    L++ FE +G L   +V     T                 
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTK---------------- 45

Query: 503 LAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGV 562
                                     +S+G          E            +      
Sbjct: 46  --------------------------RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEP 79

Query: 563 PEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 622
                  +            +++  +  ++ E  +R +F++ G I  + +   +      
Sbjct: 80  KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK- 138

Query: 623 QFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT 672
                G+ FV F   +S+++ +   +  +++ H  E++++    E  + +
Sbjct: 139 ----RGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQEMASAS 183

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.7 bits (173), Expect = 9e-16
 Identities = 20/72 (27%), Positives = 36/72 (50%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           ++V +L   VTE  L + F   GP+  + +  D  T ++ G+A V F  P  A +A   +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 399 DGTVFLGRMLHL 410
           +  V  G+ + +
Sbjct: 63  NFDVIKGKPVRI 74

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.6 bits (165), Expect = 9e-15
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
           +LY+ +L+ + TE  +   F   GPI S+ V      +      S+GY +V F       
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-----CRDMITRRSLGYAYVNFQQPADAE 56

Query: 642 QALKVLQNSSLDEHQIELKRSNRN 665
           +AL  +    +    + +  S R+
Sbjct: 57  RALDTMNFDVIKGKPVRIMWSQRD 80

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.5 bits (149), Expect = 1e-12
 Identities = 14/79 (17%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V ++     ++ + E F   G +  +R+ + M+ +    G+ +V F    +A+RA+ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-TRRSLGYAYVNFQQPADAERALD 60

Query: 747 ALCQSTHLYGRRLVLEWAE 765
            +     + G+ + + W++
Sbjct: 61  TM-NFDVIKGKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 2e-07
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
           + V +L        L   F P G +  + V    IT        V F Q   A+ A +++
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 504 AYTKFKEVPLYLEWA 518
            +   K  P+ + W+
Sbjct: 63  NFDVIKGKPVRIMWS 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 4e-06
 Identities = 11/67 (16%), Positives = 29/67 (43%), Gaps = 1/67 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            +T+  L  KF   G +  +++ +     +   +A++ + +   A+ ALD  N   +  
Sbjct: 10 PDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG 69

Query: 86 SRIKVEK 92
            +++  
Sbjct: 70 KPVRIMW 76

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 9/79 (11%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKP--------LPLASVRTTFLGMAYIGFKDEKNCNKALNK 277
           ++ V +L   V +  L   F P        +    +    LG AY+ F+   +  +AL+ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 278 -NKSFWKGKQLNIYKYSKD 295
            N    KGK + I    +D
Sbjct: 62  MNFDVIKGKPVRIMWSQRD 80

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.5 bits (172), Expect = 2e-15
 Identities = 51/85 (60%), Positives = 63/85 (74%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           + SGR+FVRNLSYT +E+DL KLF  YGPL+E+  PID  T K KGFA VTF+ PEHA +
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
           AY  +DG VF GRMLH++P   K+ 
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTIKKE 90

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.6 bits (128), Expect = 2e-09
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 5/93 (5%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
                 L+++NL++ S+E+ + + F   GP++ +                 G+ FV F  
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-----TKKPKGFAFVTFMF 59

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESE 669
            E   +A   +         + +  S    E+ 
Sbjct: 60  PEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.9 bits (116), Expect = 6e-08
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
            ++ VRN+ + + + ++E+LF A+G L  +  P   +     +GF FV F+    A +A 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKK-PKGFAFVTFMFPEHAVKAY 67

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
             +       GR L +  +  
Sbjct: 68  AEV-DGQVFQGRMLHVLPSTI 87

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 6/75 (8%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSL 503
           + V+NL Y +   DL+ LF  +G L  +  P             V F+    A  A+  +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 504 AYTKFKEVPLYLEWA 518
               F+   L++  +
Sbjct: 71  DGQVFQGRMLHVLPS 85

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.8 bits (168), Expect = 6e-15
 Identities = 22/78 (28%), Positives = 42/78 (53%)

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           + +S  ++V NLS+  TE+ + +LF K G + ++I+ +DK      GF  V +     A 
Sbjct: 4   LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 393 QAYQHLDGTVFLGRMLHL 410
            A ++++GT    R++  
Sbjct: 64  NAMRYINGTRLDDRIIRT 81

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
           +    + V N+ F   + ++ ELF   G++K + +    +      GF FVE+ ++ +A+
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KKTACGFCFVEYYSRADAE 63

Query: 743 RAMKALCQSTHLYGRRLVLEWA 764
            AM+ +   T L  R +  +W 
Sbjct: 64  NAMRYI-NGTRLDDRIIRTDWD 84

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.7 bits (134), Expect = 2e-10
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 5/86 (5%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
           E+  +   TLY+ NL+F +TE+ I   F K G I  + +   K  K+       G+ FV+
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA-----CGFCFVE 55

Query: 634 FYTRESLNQALKVLQNSSLDEHQIEL 659
           +Y+R     A++ +  + LD+  I  
Sbjct: 56  YYSRADAENAMRYINGTRLDDRIIRT 81

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (94), Expect = 6e-05
 Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSL 503
           + V NL + T    +  LF   GD+ ++++              VE+  +  A+ A   +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 504 AYTKFKEVPLYLEWAP 519
             T+  +  +  +W  
Sbjct: 70  NGTRLDDRIIRTDWDA 85

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          +  T+EQ+   F + G +  + +     +     F F+ Y+    A+ A+ Y N T +  
Sbjct: 17 FYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD 76

Query: 86 SRIKVE 91
            I+ +
Sbjct: 77 RIIRTD 82

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.5 bits (167), Expect = 6e-15
 Identities = 28/84 (33%), Positives = 45/84 (53%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++  I V NLS    E DL +LF  +G ++ + L  DK T ++KGFA ++F   E A +A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 395 YQHLDGTVFLGRMLHLIPGKPKEN 418
              + G  +   +L++   KP  N
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPSTN 90

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 18/88 (20%), Positives = 42/88 (47%), Gaps = 5/88 (5%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           R  + + T+ + NL+ ++ E  ++  F+  G I+ + +A+ K         S G+ F+ F
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTT-----GQSKGFAFISF 57

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRS 662
           + RE   +A+  +     D   + ++ +
Sbjct: 58  HRREDAARAIAGVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 1e-07
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 2/84 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + I V N+    ++++++ELF+ FG +  +    K   +G  +GF F+ F  + +A RA+
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIY-LAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 746 KALCQSTHLYGRRLVLEWAEEADN 769
             +          L +EWA+ + N
Sbjct: 68  AGV-SGFGYDHLILNVEWAKPSTN 90

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQA 496
            A     I V NL   T  TDL+ LF PFG + R+ +     T        + F ++  A
Sbjct: 4   RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 63

Query: 497 KAAFNSLAYTKFKEVPLYLEWA 518
             A   ++   +  + L +EWA
Sbjct: 64  ARAIAGVSGFGYDHLILNVEWA 85

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.0 bits (166), Expect = 6e-15
 Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           G++ V NL + V++ D+ +LF ++G L +  +  D+ + ++ G A V F     A +A +
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK 59

Query: 397 HLDGTVFLGRMLHL 410
             +G    GR +++
Sbjct: 60  QYNGVPLDGRPMNI 73

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.4 bits (141), Expect = 2e-11
 Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+LV N+ F    ++++ELF  FG LK   +      SG   G   V F  K +A +AMK
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR--SGRSLGTADVHFERKADALKAMK 59

Query: 747 ALCQSTHLYGRRLVLEWA 764
                  L GR + ++  
Sbjct: 60  QY-NGVPLDGRPMNIQLV 76

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.6 bits (131), Expect = 4e-10
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L + NL+F  ++  I+  F + G +    V   +  +      S+G   V F  +    +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR------SLGTADVHFERKADALK 56

Query: 643 ALKVLQNSSLDEHQIELK 660
           A+K      LD   + ++
Sbjct: 57  AMKQYNGVPLDGRPMNIQ 74

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.8 bits (111), Expect = 2e-07
 Identities = 11/65 (16%), Positives = 28/65 (43%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          + ++   ++  F E GT+    + Y   G+    A + + R+  A  A+  +N   +   
Sbjct: 10 FGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 69

Query: 87 RIKVE 91
           + ++
Sbjct: 70 PMNIQ 74

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.0 bits (101), Expect = 4e-06
 Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-----PYGITGLVEFLQKNQAKAAFNSLA 504
           +LV NL +     D++ LF  FG L +  V          T  V F +K  A  A     
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 505 YTKFKEVPLYLEWAP 519
                  P+ ++   
Sbjct: 63  GVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 8/71 (11%)

Query: 227 IVVKNLPAGVKKKDLKAYFKPLP-------LASVRTTFLGMAYIGFKDEKNCNKALNK-N 278
           ++V NL  GV   D++  F                   LG A + F+ + +  KA+ + N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 279 KSFWKGKQLNI 289
                G+ +NI
Sbjct: 63  GVPLDGRPMNI 73

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.0 bits (163), Expect = 2e-14
 Identities = 19/75 (25%), Positives = 31/75 (41%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
              I V+N+ +TV+ D++   F  Y  +   +     E     G A+V F   + AT A 
Sbjct: 9   PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 396 QHLDGTVFLGRMLHL 410
             L+      R + L
Sbjct: 69  IDLNDRPIGSRKVKL 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.9 bits (129), Expect = 7e-10
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 6/85 (7%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           +P P T + ++N+ F  + D I   F     I      +  +     + +  G   V F 
Sbjct: 6   KPGP-TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-----KGMPTGEAMVAFE 59

Query: 636 TRESLNQALKVLQNSSLDEHQIELK 660
           +R+    A+  L +  +   +++L 
Sbjct: 60  SRDEATAAVIDLNDRPIGSRKVKLV 84

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 2/87 (2%)

Query: 678 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 737
           ++  K   + I V+N+PF     E+ + F  +  +      K     G+  G   V F +
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAFES 60

Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWA 764
           ++EA  A+  L     +  R++ L   
Sbjct: 61  RDEATAAVIDL-NDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 27 YKITQEQLKAKFEEKG-TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
          + ++ +++   F         V LKY  +G     A + +   D+A AA+   N+  + S
Sbjct: 19 FTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS 78

Query: 86 SRIKVE 91
           ++K+ 
Sbjct: 79 RKVKLV 84

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 66.5 bits (162), Expect = 3e-14
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           E I ++  ++V NL  T+T+D L  +F KYG + +  +  DK T + +G A V +   E 
Sbjct: 2   ESIKDT-NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 391 ATQAYQHLDGTVFLGR 406
           A +A   L+  +  G 
Sbjct: 61  AQEAISALNNVIPEGG 76

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 60.0 bits (145), Expect = 6e-12
 Identities = 23/85 (27%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           E   DT LY+ NL    T+D +   F K G I      +K   +        G  FV++ 
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSI-----VQKNILRDKLTGRPRGVAFVRYN 56

Query: 636 TRESLNQALKVLQNSSLDEHQIELK 660
            RE   +A+  L N   +     L 
Sbjct: 57  KREEAQEAISALNNVIPEGGSQPLS 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 54.6 bits (131), Expect = 4e-10
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            + + V N+P      +++ +F  +G +       +   +G  RG  FV +  + EA+ A
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN-ILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 745 MKALCQST-HLYGRRLVLEWA 764
           + AL         + L +  A
Sbjct: 65  ISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQA 496
           E+     + V NLP       L  +F  +G + +  +    +T        V + ++ +A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 497 KAAFNSLAYTKFK--EVPLYLEWA 518
           + A ++L     +    PL +  A
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.3 bits (94), Expect = 4e-05
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKF-RRFAFIGYHREDQAQAALDYFNNTYVF- 84
            IT +QL   F + G++    +         R  AF+ Y++ ++AQ A+   NN     
Sbjct: 16 RTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG 75

Query: 85 -SSRIKVE 91
           S  + V 
Sbjct: 76 GSQPLSVR 83

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.2 bits (161), Expect = 3e-14
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKE---TDKTKGFALVTFLMPEHATQAY 395
           +F++NL+++ TE+ L  +F K G +    +   K       + GF  V +  PE A +A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
           + L G    G  L +   +   
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.4 bits (151), Expect = 1e-12
 Identities = 33/82 (40%), Positives = 54/82 (65%), Gaps = 2/82 (2%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+IKNLNF++TE++++  F K G I S T+++KK+         MG+GFV++   E   +
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLS--MGFGFVEYKKPEQAQK 58

Query: 643 ALKVLQNSSLDEHQIELKRSNR 664
           ALK LQ  ++D H++E++ S R
Sbjct: 59  ALKQLQGHTVDGHKLEVRISER 80

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.3 bits (143), Expect = 1e-11
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + ++N+ F   +  ++ +F   G +K   +   K   G  L  GFGFVE+    +A++A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 746 KALCQSTHLYGRRLVLEWAEEAD 768
           K L Q   + G +L +  +E A 
Sbjct: 61  KQL-QGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.5 bits (102), Expect = 3e-06
 Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQL----KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
          +  T+E LK  F + G +    +              F F+ Y + +QAQ AL       
Sbjct: 8  FSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT 67

Query: 83 VFSSRIKVEK 92
          V   +++V  
Sbjct: 68 VDGHKLEVRI 77

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 9/78 (11%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP---------PYGITGLVEFLQKNQAKAAF 500
           + +KNL + T    LK +F   G +    +               G VE+ +  QA+ A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 501 NSLAYTKFKEVPLYLEWA 518
             L         L +  +
Sbjct: 61  KQLQGHTVDGHKLEVRIS 78

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.3 bits (161), Expect = 4e-14
 Identities = 26/85 (30%), Positives = 47/85 (55%)

Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
           ++ G++FV  LS+   E  L ++F KYG ++EV++  D+ET +++GF  VTF   + A  
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
           A   ++G    GR + +       +
Sbjct: 63  AMMAMNGKSVDGRQIRVDQAGKSSD 87

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           +  L++  L+F++ E S+ + F K G I     +     K      S G+GFV F   + 
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQI-----SEVVVVKDRETQRSRGFGFVTFENIDD 59

Query: 640 LNQALKVLQNSSLDEHQIELKRSNR 664
              A+  +   S+D  QI + ++ +
Sbjct: 60  AKDAMMAMNGKSVDGRQIRVDQAGK 84

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ V  + F   +  +E++F  +G++  V    K   +   RGFGFV F   ++AK AM 
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVV-VVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 747 ALCQSTHLYGRRLVLEWAEE 766
           A+     + GR++ ++ A +
Sbjct: 66  AM-NGKSVDGRQIRVDQAGK 84

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.3 bits (161), Expect = 6e-14
 Identities = 28/99 (28%), Positives = 47/99 (47%), Gaps = 8/99 (8%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP--------IDKETDKTKGFAL 382
           ++ +++  I+V+ L+ +VT DDL   F++ G +              +DKET K KG A 
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 383 VTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
           V++  P  A  A +  DG  F G  L +   + K    +
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (131), Expect = 6e-10
 Identities = 13/93 (13%), Positives = 33/93 (35%), Gaps = 3/93 (3%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK---KDPKSPGQFLSMGYGFV 632
           E   ++ +Y++ LN + T D +   FK+CG +       +               G   V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
            +    +   A++          ++++  + + 
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 8e-07
 Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-------GSGLHRGFGFVEFIT 737
            S I V+ +       ++ + FK  G +K  +   + +        +G  +G   V +  
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
              AK A++         G +L +  A +
Sbjct: 68  PPTAKAAVEWF-DGKDFQGSKLKVSLARK 95

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 65.4 bits (159), Expect = 7e-14
 Identities = 19/78 (24%), Positives = 35/78 (44%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            + V  L   +T+ +L  LF   GP+    +  D +T  + G+A V F     + +A + 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 398 LDGTVFLGRMLHLIPGKP 415
           L+G     + L +   +P
Sbjct: 64  LNGITVRNKRLKVSYARP 81

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           +T L +  L  + T+  +   F+  GPI +  + R           S GY FV F +   
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGY-----SYGYAFVDFTSEMD 56

Query: 640 LNQALKVLQNSSLDEHQIELKRS 662
             +A+KVL   ++   ++++  +
Sbjct: 57  SQRAIKVLNGITVRNKRLKVSYA 79

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 55.4 bits (133), Expect = 2e-10
 Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           + + ++V  +P      E+  LF+A G +   R+ +    +G   G+ FV+F ++ +++R
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK-TGYSYGYAFVDFTSEMDSQR 59

Query: 744 AMKALCQSTHLYGRRLVLEWA 764
           A+K L     +  +RL + +A
Sbjct: 60  AIKVL-NGITVRNKRLKVSYA 79

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 45.8 bits (108), Expect = 6e-07
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 499
           S   ++V  LP      +L ALF   G +    +     TG       V+F  +  ++ A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 500 FNSLAYTKFKEVPLYLEWAPEG 521
              L     +   L + +A  G
Sbjct: 61  IKVLNGITVRNKRLKVSYARPG 82

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 27 YKITQEQLKAKFEEKGTVTDV-QLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
            +T  +L A F   G +     ++    G    +AF+ +  E  +Q A+   N   V +
Sbjct: 12 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN 71

Query: 86 SRIKVEK 92
           R+KV  
Sbjct: 72 KRLKVSY 78

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 7e-14
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            + V  LS   TE DL ++F KYGP+A+V +  D+++ +++GFA V F   + A +A + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 398 LDGTVFLGRMLH 409
            +G    GR + 
Sbjct: 71  ANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 6e-11
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
            P+P+  L +  L+  +TE  +R  F K GPIA V++   +         S G+ FV F 
Sbjct: 5   NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-----SRRSRGFAFVYFE 59

Query: 636 TRESLNQALKVLQNSSLDEHQIE 658
             +   +A +      LD  +I 
Sbjct: 60  NVDDAKEAKERANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
              + V  +     + ++ E+F  +G +  V +      S   RGF FV F   ++AK A
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRRSRGFAFVYFENVDDAKEA 67

Query: 745 MKALCQSTHLYGRRL 759
            +       L GRR+
Sbjct: 68  KERA-NGMELDGRRI 81

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (159), Expect = 8e-14
 Identities = 18/73 (24%), Positives = 36/73 (49%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            ++V  L  T+T+ +L +LF +YG +    + +D+ T  ++G   + F     A +A + 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 398 LDGTVFLGRMLHL 410
           L+G    G    +
Sbjct: 68  LNGQKPSGATEPI 80

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 7e-11
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           D  LY+  L    T+  + + F + G I +  +   +        +S G GF++F  R  
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-----TGVSRGVGFIRFDKRIE 60

Query: 640 LNQALKVLQNSSLDEHQIELK 660
             +A+K L           + 
Sbjct: 61  AEEAIKGLNGQKPSGATEPIT 81

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            + + V  +P    Q E+E+LF  +G +   R+    V     RG GF+ F  + EA+ A
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGV-SRGVGFIRFDKRIEAEEA 64

Query: 745 MKALCQSTHLYGR--RLVLEWA 764
           +K L       G    + +++A
Sbjct: 65  IKGL-NGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
           + V  LP      +L+ LF  +G +    +    +T      G + F ++ +A+ A   L
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 504 AYTKF--KEVPLYLEWA 518
              K      P+ +++A
Sbjct: 69  NGQKPSGATEPITVKFA 85

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (160), Expect = 8e-14
 Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
             + +  ++  +F   L+  +   DL   F   G + +V +  D+ + ++KG A V F  
Sbjct: 10  NLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 69

Query: 388 PEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            +        L G   LG  + +   + ++N
Sbjct: 70  IQSV-PLAIGLTGQRLLGVPIIVQASQAEKN 99

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 6e-08
 Identities = 16/94 (17%), Positives = 32/94 (34%), Gaps = 6/94 (6%)

Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
            ++   E     T++   L        +   F   G +  V +   ++        S G 
Sbjct: 8   VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN-----SRRSKGI 62

Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
            +V+F   +S+  A+  L    L    I ++ S 
Sbjct: 63  AYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ 95

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 5e-06
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            +    +  + +  ++E+ F A G+++ VR+      S   +G  +VEF        A+ 
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN-SRRSKGIAYVEFCEIQSVPLAIG 78

Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
                  L G  ++++ ++   N
Sbjct: 79  --LTGQRLLGVPIIVQASQAEKN 99

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 209 PSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT-------FLGM 260
           P   PV      +R   T+    L A ++ +DL+ +F  +  +  VR           G+
Sbjct: 3   PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 62

Query: 261 AYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
           AY+ F + ++   A+        G  + +
Sbjct: 63  AYVEFCEIQSVPLAIGLTGQRLLGVPIIV 91

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.3 bits (159), Expect = 1e-13
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 9/82 (10%)

Query: 338 RIFVRNLS-YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
           R+F+ NL+   V + D+  +F KYG +              KGFA V ++   +A  A  
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGC--------SVHKGFAFVQYVNERNARAAVA 68

Query: 397 HLDGTVFLGRMLHLIPGKPKEN 418
             DG +  G++L +      + 
Sbjct: 69  GEDGRMIAGQVLDINLAAEPKV 90

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.4 bits (149), Expect = 2e-12
 Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 11/86 (12%)

Query: 682 KQTGSKILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
           +   S++ + N+     K+S+VE +F  +G++    +         H+GF FV+++ +  
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---------HKGFAFVQYVNERN 62

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEE 766
           A+ A+        + G+ L +  A E
Sbjct: 63  ARAAVAGE-DGRMIAGQVLDINLAAE 87

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.6 bits (134), Expect = 2e-10
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 14/90 (15%)

Query: 576 EPEPDTTLYIKNLNFNSTEDS-IRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
               ++ ++I NLN    + S +   F K G I   +V               G+ FVQ+
Sbjct: 11  PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------------HKGFAFVQY 57

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNR 664
               +   A+       +    +++  +  
Sbjct: 58  VNERNARAAVAGEDGRMIAGQVLDINLAAE 87

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (101), Expect = 7e-06
 Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 7/66 (10%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
            + +  ++A F + G +    +          FAF+ Y  E  A+AA+   +   +   
Sbjct: 26 LVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARAAVAGEDGRMIAGQ 78

Query: 87 RIKVEK 92
           + +  
Sbjct: 79 VLDINL 84

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (94), Expect = 7e-05
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 450 ILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
           + + NL       +D++A+F  +G +    V        V+++ +  A+AA         
Sbjct: 18  VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--FAFVQYVNERNARAAVAGEDGRMI 75

Query: 509 KEVPLYLEWAPE 520
               L +  A E
Sbjct: 76  AGQVLDINLAAE 87

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.7 bits (157), Expect = 1e-13
 Identities = 18/83 (21%), Positives = 34/83 (40%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           + ++F+  L   + +D + +L   +GPL    L  D  T  +KG+A   ++      QA 
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 396 QHLDGTVFLGRMLHLIPGKPKEN 418
             L+G     + L +        
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGAK 83

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 1e-09
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ +  +P      +V+EL  +FG LK      K   +GL +G+ F E++  N   +A+ 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFN-LVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 747 ALCQSTHLYGRRLVLEWAE 765
            L     L  ++L+++ A 
Sbjct: 62  GL-NGMQLGDKKLLVQRAS 79

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           L+I  L     +D ++      GP+ +         K     LS GY F ++      +Q
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAF-----NLVKDSATGLSKGYAFCEYVDINVTDQ 58

Query: 643 ALKVLQNSSLDEHQIELKRSN 663
           A+  L    L + ++ ++R++
Sbjct: 59  AIAGLNGMQLGDKKLLVQRAS 79

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 6e-04
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 5/69 (7%)

Query: 27 YKITQEQLK---AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
            +  +Q+K     F        V+   T     + +AF  Y   +    A+   N   +
Sbjct: 11 NYLNDDQVKELLTSFGPLKAFNLVKDSATG--LSKGYAFCEYVDINVTDQAIAGLNGMQL 68

Query: 84 FSSRIKVEK 92
             ++ V++
Sbjct: 69 GDKKLLVQR 77

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 6e-04
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 6/78 (7%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
           + +  LP       +K L   FG L    +     T         E++  N    A   L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 504 AYTKFKEVPLYLEWAPEG 521
              +  +  L ++ A  G
Sbjct: 64  NGMQLGDKKLLVQRASVG 81

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 2e-13
 Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 333 IAESGR-IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
           +A + R ++V  L+  V +  L   F  +G + ++ +P+D ET+K +GFA V F + E A
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKEN 418
             A  +++ +   GR + +   KP   
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAKPMRI 87

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 4e-08
 Identities = 16/84 (19%), Positives = 26/84 (30%), Gaps = 5/84 (5%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
               LY+  L     +  +   F   G I        + P         G+ FV+F   E
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITD-----IQIPLDYETEKHRGFAFVEFELAE 58

Query: 639 SLNQALKVLQNSSLDEHQIELKRS 662
               A+  +  S L    I +  +
Sbjct: 59  DAAAAIDNMNESELFGRTIRVNLA 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 4e-07
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
            T   + V  +  +     +   F  FG++  +++P     +  HRGF FVEF    +A 
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAA 61

Query: 743 RAMKALCQSTHLYGRRLVLEWAE 765
            A+  +   + L+GR + +  A+
Sbjct: 62  AAIDNM-NESELFGRTIRVNLAK 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 5e-06
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAK 497
           A +KR++ V  L        L A F PFGD+  + +P    T        VEF     A 
Sbjct: 2   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 498 AAFNSLAYTKFKEVPLYLEWA 518
           AA +++  ++     + +  A
Sbjct: 62  AAIDNMNESELFGRTIRVNLA 82

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.0 bits (158), Expect = 2e-13
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 3/91 (3%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
            +  +++RNL Y +T +++  +F KYGP+ ++ +       +T+G A V +     A  A
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNA 62

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGK 425
             HL G     R L ++          +D K
Sbjct: 63  CDHLSGFNVCNRYLVVLYYNANRAFQKMDTK 93

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 7e-13
 Identities = 22/107 (20%), Positives = 39/107 (36%), Gaps = 8/107 (7%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
           PE +  LYI+NL +  T + +   F K GPI  + V    + +        G  +V +  
Sbjct: 4   PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR--------GTAYVVYED 55

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQ 683
                 A   L   ++    + +   N N   +    K+K   +   
Sbjct: 56  IFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 102

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 1e-10
 Identities = 16/97 (16%), Positives = 42/97 (43%), Gaps = 5/97 (5%)

Query: 680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 739
           +  +    + +RN+P++    E+ ++F  +G ++      ++  +   RG  +V +    
Sbjct: 2   LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ----IRVGNTPETRGTAYVVYEDIF 57

Query: 740 EAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKR 776
           +AK A   L    ++  R LV+ +       + +  +
Sbjct: 58  DAKNACDHL-SGFNVCNRYLVVLYYNANRAFQKMDTK 93

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 3e-07
 Identities = 22/107 (20%), Positives = 43/107 (40%), Gaps = 5/107 (4%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI---TGLVEFLQKNQAKAAFNSLA 504
           RI+ ++NLPY+    ++  +F  +G + ++ V        T  V +     AK A + L+
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKE--KEKNEEEGEEGEEEK 549
                   L + +       +  +  K +E  K   E+ G   +  K
Sbjct: 68  GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 114

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
          YKIT E++   F + G +  +++  T   + R  A++ Y     A+ A D+ +   V + 
Sbjct: 17 YKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNR 74

Query: 87 RIKVE 91
           + V 
Sbjct: 75 YLVVL 79

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 64.3 bits (156), Expect = 2e-13
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 5/90 (5%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           ++ +  +  +  +NLS+ +TED+L ++FE       + + +  +  K+KG A + F    
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            A +  +   G    GR + L     K   
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 51.6 bits (123), Expect = 7e-09
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 10/90 (11%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           ++     TL  KNL+FN TED ++  F+    I  V+   K            G  +++F
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKS----------KGIAYIEF 60

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNR 664
            +     + L+  Q + +D   + L  +  
Sbjct: 61  KSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 22/101 (21%), Positives = 49/101 (48%), Gaps = 14/101 (13%)

Query: 666 LESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 725
           LE   T+ K +++         +L +N+ F   + E++E+F+   E++ V         G
Sbjct: 4   LEDPCTSKKVRAAR-------TLLAKNLSFNITEDELKEVFEDALEIRLVSQD------G 50

Query: 726 LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
             +G  ++EF ++ +A++ ++   Q   + GR + L +  E
Sbjct: 51  KSKGIAYIEFKSEADAEKNLEEK-QGAEIDGRSVSLYYTGE 90

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 1/77 (1%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFN 501
           + R+ R +L KNL +     +LK +FE   ++  V           +EF  +  A+    
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 502 SLAYTKFKEVPLYLEWA 518
                +     + L + 
Sbjct: 72  EKQGAEIDGRSVSLYYT 88

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 212 PPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLP---LASVRTTFLGMAYIGFKDE 268
           P  SK     R   T++ KNL   + + +LK  F+      L S      G+AYI FK E
Sbjct: 7   PCTSKKV---RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSE 63

Query: 269 KNCNKALNK-NKSFWKGKQLNI 289
            +  K L +   +   G+ +++
Sbjct: 64  ADAEKNLEEKQGAEIDGRSVSL 85

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 3e-13
 Identities = 23/86 (26%), Positives = 31/86 (36%), Gaps = 3/86 (3%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
              RI+V NL   +   D+  +F KYG    +     K       FA V F  P  A  A
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGA---IRDIDLKNRRGGPPFAFVEFEDPRDAEDA 69

Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEG 420
               DG  + G  L +   +     G
Sbjct: 70  VYGRDGYDYDGYRLRVEFPRSGRGTG 95

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 3e-10
 Identities = 18/92 (19%), Positives = 31/92 (33%), Gaps = 10/92 (10%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
               D  +Y+ NL  +     I   F K G I  + +  ++            + FV+F 
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP--------PFAFVEFE 61

Query: 636 TRESLNQALKVLQNSSLDEHQI--ELKRSNRN 665
                  A+        D +++  E  RS R 
Sbjct: 62  DPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 93

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 4e-09
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
           A     +I V N+P   +  ++E++F  +G ++ + L  +         F FVEF    +
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG----GPPFAFVEFEDPRD 65

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEE 766
           A+ A+          G RL +E+   
Sbjct: 66  AEDAVYGR-DGYDYDGYRLRVEFPRS 90

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP---PYGITGLVEFLQKNQAKAAFNSLAYT 506
           I V NLP      D++ +F  +G +  + +           VEF     A+ A       
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query: 507 KFKEVPLYLEWAPEG 521
            +    L +E+   G
Sbjct: 77  DYDGYRLRVEFPRSG 91

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 7/75 (9%)

Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASV-----RTTFLGMAYIGFKDEKNCNKALNK-NK 279
            I V NLP  ++ KD++  F             R      A++ F+D ++   A+   + 
Sbjct: 16  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 75

Query: 280 SFWKGKQLNIYKYSK 294
             + G +L + ++ +
Sbjct: 76  YDYDGYRLRV-EFPR 89

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.6 bits (154), Expect = 3e-13
 Identities = 18/78 (23%), Positives = 36/78 (46%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            + V  L   +T+++   LF   G +    L  DK T ++ G+  V ++ P+ A +A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 398 LDGTVFLGRMLHLIPGKP 415
           L+G     + + +   +P
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + ++V  +P    Q E   LF + GE++  +L +  + +G   G+GFV +I   +A++A+
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-TGQSLGYGFVNYIDPKDAEKAI 61

Query: 746 KALCQSTHLYGRRLVLEWAE 765
             L     L  + + + +A 
Sbjct: 62  NTL-NGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           T L +  L  N T++  R  F   G I S  + R K          +GYGFV +   +  
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQS-----LGYGFVNYIDPKDA 57

Query: 641 NQALKVLQNSSLDEHQIELKRS 662
            +A+  L    L    I++  +
Sbjct: 58  EKAINTLNGLRLQTKTIKVSYA 79

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 499
           SK  ++V  LP      + ++LF   G++    +    ITG       V ++    A+ A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 500 FNSLAYTKFKEVPLYLEWA 518
            N+L   + +   + + +A
Sbjct: 61  INTLNGLRLQTKTIKVSYA 79

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 3e-13
 Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           ED  +   ++V NLS  VTE  + +LF + GP     +  +  ++    F  V F     
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF--VEFYEHRD 60

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
           A  A   ++G   LG+ + +       ++
Sbjct: 61  AAAALAAMNGRKILGKEVKVNWATTPSSQ 89

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 2e-09
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 7/89 (7%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           +     TLY+ NL+ + TE  I + F + GP  S  +  +             Y FV+FY
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-------DPYCFVEFY 56

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNR 664
                  AL  +    +   ++++  +  
Sbjct: 57  EHRDAAAALAAMNGRKILGKEVKVNWATT 85

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V N+     +  + +LF   G  K  +    +     +  + FVEF    +A  A+ 
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKSCK---MITEHTSNDPYCFVEFYEHRDAAAALA 66

Query: 747 ALCQSTHLYGRRLVLEWAE 765
           A+     + G+ + + WA 
Sbjct: 67  AM-NGRKILGKEVKVNWAT 84

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 16/80 (20%), Positives = 25/80 (31%), Gaps = 4/80 (5%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP----PYGITGLVEFLQKNQAKA 498
           +    R + V NL        +  LF   G      +            VEF +   A A
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 499 AFNSLAYTKFKEVPLYLEWA 518
           A  ++   K     + + WA
Sbjct: 64  ALAAMNGRKILGKEVKVNWA 83

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 6e-13
 Identities = 16/84 (19%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           ++  ++   ++  +T+  + + F  +G + E+ +         KG++ V F   E A  A
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHA 70

Query: 395 YQHLDGTVFLGRMLHLIPGKPKEN 418
              ++GT   G ++    GK   +
Sbjct: 71  IVSVNGTTIEGHVVKCYWGKESPD 94

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.5 bits (136), Expect = 1e-10
 Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 8/88 (9%)

Query: 679 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 738
           N +      +    I        + + F  FG++  +R+          +G+ FV F T 
Sbjct: 12  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-------EKGYSFVRFSTH 64

Query: 739 NEAKRAMKALCQSTHLYGRRLVLEWAEE 766
             A  A+ ++   T + G  +   W +E
Sbjct: 65  ESAAHAIVSV-NGTTIEGHVVKCYWGKE 91

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 11/98 (11%)

Query: 568 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 627
             E+   +    + T+Y   +    T+  +R+ F   G I  + V  +            
Sbjct: 6   RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----------K 54

Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
           GY FV+F T ES   A+  +  ++++ H ++      +
Sbjct: 55  GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 16/83 (19%), Positives = 26/83 (31%), Gaps = 2/83 (2%)

Query: 438 FNQVVE--ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQ 495
           F  VV   +     +    +        ++  F PFG +  + V P      V F     
Sbjct: 7   FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHES 66

Query: 496 AKAAFNSLAYTKFKEVPLYLEWA 518
           A  A  S+  T  +   +   W 
Sbjct: 67  AAHAIVSVNGTTIEGHVVKCYWG 89

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 13/87 (14%), Positives = 33/87 (37%), Gaps = 18/87 (20%)

Query: 27  YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             +T + ++  F   G + ++++        + ++F+ +   + A  A+   N T +   
Sbjct: 28  SGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNGTTIEGH 82

Query: 87  RIKVEKCSNLGDTTKPKSWSKYAPDSS 113
            +K               W K +PD +
Sbjct: 83  VVKC-------------YWGKESPDMT 96

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.3 bits (151), Expect = 6e-13
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++F+  LS+  T++ L + F ++G + E ++  D  T +++GF  VTF+      +    
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 398 LDGTVFLGRMLH 409
                   + + 
Sbjct: 61  QSRHELDSKTID 72

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ +  + +Q  Q  + E F  FGE+K      +   +   RGFGFV F+ +    + + 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECL-VMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 747 ALCQSTHLYGRRLVLEWA 764
                  L  + +  + A
Sbjct: 61  Q--SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++I  L++ +T++ +R +F + G +           + P    S G+GFV F  +  +++
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV-----KECLVMRDPLTKRSRGFGFVTFMDQAGVDK 57

Query: 643 ALKVLQNSSLDEHQIELKR 661
            L       LD   I+ K 
Sbjct: 58  VLA-QSRHELDSKTIDPKV 75

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 10/71 (14%), Positives = 24/71 (33%), Gaps = 8/71 (11%)

Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALNKN 278
           + +  L     ++ L+ YF                     G  ++ F D+   +K L ++
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 279 KSFWKGKQLNI 289
           +     K ++ 
Sbjct: 63  RHELDSKTIDP 73

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.7 bits (152), Expect = 7e-13
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +   ++V  L   V+E  L +LF + GP+    +P D+ T + +G+  V FL  E A  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 395 YQHLDGTVFLGRMLHLIPGKPKEN 418
            + +D     G+ + +        
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 6e-12
 Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 5/90 (5%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           E   D T+Y+  L+   +E  +   F + GP+ +        PK        GYGFV+F 
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVN-----THMPKDRVTGQHQGYGFVEFL 59

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNRN 665
           + E  + A+K++    L    I + +++ +
Sbjct: 60  SEEDADYAIKIMDMIKLYGKPIRVNKASAH 89

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V  +  +  +  + ELF   G +       K   +G H+G+GFVEF+++ +A  A+K
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTH-MPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
            +     LYG+ + +  A   + 
Sbjct: 70  IM-DMIKLYGKPIRVNKASAHNK 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 19/82 (23%), Positives = 28/82 (34%), Gaps = 6/82 (7%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQA 496
           E      + V  L  +     L  LF   G +    +P   +T      G VEFL +  A
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 497 KAAFNSLAYTKFKEVPLYLEWA 518
             A   +   K    P+ +  A
Sbjct: 65  DYAIKIMDMIKLYGKPIRVNKA 86

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.9 bits (152), Expect = 1e-12
 Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           + D A  G + +R L +  +++++ + F     +   +        ++ G A V F   E
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKE 417
            A +            R + +      E
Sbjct: 69  IA-EKALKKHKERIGHRYIEIFKSSRAE 95

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 2e-05
 Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
                 + +R +PF   + E+ + F     +            G   G  FV+F ++  A
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIA 70

Query: 742 KRAMKALCQSTHLYGRRLVLEWAEEAD 768
           ++A+K       +  R + +  +  A+
Sbjct: 71  EKALK--KHKERIGHRYIEIFKSSRAE 95

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.7 bits (149), Expect = 1e-12
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPL-AEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           IF+ NL   + E  L   F  +G +     +  D +T  +KG+A + F   + +  A + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 398 LDGTVFLGRMLHLIPGKPKENEG 420
           ++G     R + +     K+++G
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSKG 83

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 7e-11
 Identities = 16/82 (19%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           I + N+  +  +  + + F AFG +       +   +G  +G+ F+ F + + +  A++A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 748 LCQSTHLYGRRLVLEWAEEADN 769
                +L  R + + +A + D+
Sbjct: 61  -MNGQYLCNRPITVSYAFKKDS 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 3e-09
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++I NL+    E  +   F   G I    +   K  + P    S GY F+ F + ++ + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFASFDASDA 56

Query: 643 ALKVLQNSSLDEHQIELKRSNR 664
           A++ +    L    I +  + +
Sbjct: 57  AIEAMNGQYLCNRPITVSYAFK 78

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 5e-04
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR--FAFIGYHREDQAQAALDYFNNTYVF 84
           +I ++ L   F   G +                 +AFI +   D + AA++  N  Y+ 
Sbjct: 8  PEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC 67

Query: 85 SSRIKVEK 92
          +  I V  
Sbjct: 68 NRPITVSY 75

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 0.001
 Identities = 12/76 (15%), Positives = 23/76 (30%), Gaps = 7/76 (9%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-------TGLVEFLQKNQAKAAFNS 502
           I + NL        L   F  FG + +                  + F   + + AA  +
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 503 LAYTKFKEVPLYLEWA 518
           +        P+ + +A
Sbjct: 61  MNGQYLCNRPITVSYA 76

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.5 bits (149), Expect = 2e-12
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 2/86 (2%)

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           + ++  + V  L +  TE DL + F  +G +  V +  D +T  +KGF  V F   E   
Sbjct: 5   VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKEN 418
           +           GR         K++
Sbjct: 65  KVMSQRHM--IDGRWCDCKLPNSKQS 88

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.5 bits (136), Expect = 1e-10
 Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 7/91 (7%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
           +R  +  + L +  L + +TE  ++ +F   G +        +  K      S G+GFV+
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLM-----VQVKKDLKTGHSKGFGFVR 56

Query: 634 FYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
           F   E+  + +   Q   +D    + K  N 
Sbjct: 57  FTEYETQVKVMS--QRHMIDGRWCDCKLPNS 85

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 3e-09
 Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 9/94 (9%)

Query: 673 VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
           VKR     A Q  S ++V  +P++  + +++E F  FGE+  V++ K +  +G  +GFGF
Sbjct: 1   VKR-----AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK-TGHSKGFGF 54

Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
           V F       + M        + GR    +    
Sbjct: 55  VRFTEYETQVKVMSQR---HMIDGRWCDCKLPNS 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 2e-12
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
            G IF++NL  ++    L   F  +G +    +  D+   K  GF  V F   E A +A 
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF--VHFETQEAAERAI 65

Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
           + ++G +   R + +   K ++
Sbjct: 66  EKMNGMLLNDRKVFVGRFKSRK 87

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 7e-09
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
           K     I ++N+        + + F AFG +   ++     GS  +    FV F T+  A
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYG---FVHFETQEAA 61

Query: 742 KRAMKALCQSTHLYGRRLVLEWAEE 766
           +RA++ +     L  R++ +   + 
Sbjct: 62  ERAIEKM-NGMLLNDRKVFVGRFKS 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
             ++IKNL+ +    ++   F   G I S  V          +  S GYGFV F T+E+ 
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-------ENGSKGYGFVHFETQEAA 61

Query: 641 NQALKVLQNSSLDEHQIELKRSNR 664
            +A++ +    L++ ++ + R   
Sbjct: 62  ERAIEKMNGMLLNDRKVFVGRFKS 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 13/73 (17%), Positives = 23/73 (31%), Gaps = 4/73 (5%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG----LVEFLQKNQAKAAFNSLAY 505
           I +KNL        L   F  FG++    V            V F  +  A+ A   +  
Sbjct: 11  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 70

Query: 506 TKFKEVPLYLEWA 518
               +  +++   
Sbjct: 71  MLLNDRKVFVGRF 83

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 3e-12
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           +E  +   R+ V N+ +   + DL ++F ++G + +V +  ++   K  GF  VTF    
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGF--VTFENSA 62

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
            A +A + L GTV  GR + +     +  
Sbjct: 63  DADRAREKLHGTVVEGRKIEVNNATARVM 91

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 11/98 (11%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
           +K T  ++ V NIPF+ +  ++ ++F  F     +   + +      +GFGFV F    +
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQF---GKILDVEIIFNERGSKGFGFVTFENSAD 63

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTN 778
           A RA + L   T + GR++ +  A         R  TN
Sbjct: 64  ADRAREKL-HGTVVEGRKIEVNNATA-------RVMTN 93

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
                  L++ N+ F   +  +R+ F + G I  V +   +         S G+GFV F 
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-------SKGFGFVTFE 59

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSN 663
                ++A + L  + ++  +IE+  + 
Sbjct: 60  NSADADRAREKLHGTVVEGRKIEVNNAT 87

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 5e-12
 Identities = 13/85 (15%), Positives = 30/85 (35%), Gaps = 4/85 (4%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVI--LPIDKETDKTKGFALVTFLMPEHATQAY 395
           R+F+  +      +++ +   K       +       +  K +GFA V +     A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 396 QHLDGTVFL--GRMLHLIPGKPKEN 418
           + L        G  + +   +P+ +
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEID 87

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 1e-11
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 2/89 (2%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
            ++ +  IP   K+ E+ E      E    V +         +RGF FVE+ +   A  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 745 MKALCQSTH-LYGRRLVLEWAEEADNVED 772
            + L      L+G ++ ++WAE   +V++
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDE 90

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 13/85 (15%), Positives = 26/85 (30%), Gaps = 5/85 (5%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
             L+I  +      + I     K        +             + G+ FV++ +  + 
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADK---MKNRGFAFVEYESHRAA 58

Query: 641 NQALKVLQNSS--LDEHQIELKRSN 663
             A + L      L  HQI +  + 
Sbjct: 59  AMARRKLMPGRIQLWGHQIAVDWAE 83

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.1 bits (147), Expect = 5e-12
 Identities = 54/103 (52%), Positives = 68/103 (66%), Gaps = 1/103 (0%)

Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 502
             RSK +IL KNLP  TL  +++  F  FG LGRVL+P  GIT +VEFL+  +A+ AF  
Sbjct: 6   SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRH 65

Query: 503 LAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEG 545
           LAY+KF  VPLYLEWAP GVF  A +K K  + E+  E+ E G
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQK-KDSQHEQPAEKAESG 107

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.3 bits (106), Expect = 1e-06
 Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 8/103 (7%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
           SS  + ++ + IL +N+P     +E++E F  FG L  V LP+             VEF+
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-------GGITAIVEFL 54

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
              EA++A + L   +  +   L LEWA         +K+ ++
Sbjct: 55  EPLEARKAFRHL-AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQ 96

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (101), Expect = 8e-06
 Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I  +NL       ++ + F ++G L  V+LP           A+V FL P  A +A++HL
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKAFRHL 66

Query: 399 DGTVFLGRMLHLIPGKPKENEGNVDGK 425
             + F    L+L              K
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKK 93

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.6 bits (99), Expect = 2e-05
 Identities = 16/106 (15%), Positives = 29/106 (27%), Gaps = 11/106 (10%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
             T +  KNL   +    I+  F + G +  V                     V+F    
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL-----------LPEGGITAIVEFLEPL 57

Query: 639 SLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQT 684
              +A + L  S      + L+ +   +   A   K        + 
Sbjct: 58  EARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEK 103

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 7e-12
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++F+  LS+  TE+ L   +E++G L + ++  D  + +++GF  VTF        A   
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA- 80

Query: 398 LDGTVFLGRMLHLIPGKPKENEG 420
                  GR++       +E  G
Sbjct: 81  ARPHSIDGRVVEPKRAVAREESG 103

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 1e-11
 Identities = 29/105 (27%), Positives = 52/105 (49%), Gaps = 6/105 (5%)

Query: 564 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
            +E    E ++RE E    L+I  L+F +TE+S+R ++++ G +           + P  
Sbjct: 4   TLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKL-----TDCVVMRDPAS 58

Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLES 668
             S G+GFV F +   ++ A+   +  S+D   +E KR+    ES
Sbjct: 59  KRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES 102

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 6e-10
 Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 3/99 (3%)

Query: 666 LESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 725
           +E    TV  +     K+   K+ +  + F+  +  +   ++ +G+L       +   S 
Sbjct: 1   MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV-VMRDPASK 59

Query: 726 LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
             RGFGFV F +  E   AM A  +   + GR +  + A
Sbjct: 60  RSRGFGFVTFSSMAEVDAAMAA--RPHSIDGRVVEPKRA 96

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 10/87 (11%), Positives = 27/87 (31%), Gaps = 8/87 (9%)

Query: 211 VPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAY 262
             P+ +    K Q+  + +  L     ++ L+ Y++     +              G  +
Sbjct: 7   TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 263 IGFKDEKNCNKALNKNKSFWKGKQLNI 289
           + F      + A+        G+ +  
Sbjct: 67  VTFSSMAEVDAAMAARPHSIDGRVVEP 93

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 59.7 bits (144), Expect = 7e-12
 Identities = 22/82 (26%), Positives = 42/82 (51%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           E   +FV ++     ED++ + F  YG +  + L +D+ T  +KG+ALV +   + A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 395 YQHLDGTVFLGRMLHLIPGKPK 416
            + L+G   +G+ + +     K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 48.6 bits (115), Expect = 8e-08
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G  + V +I  +A++ E++E F  +GE            +G  +G+  VE+ T  +A  A
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGE-IKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 745 MKALCQSTHLYGRRLVLEWA 764
            +AL     + G+ + ++W 
Sbjct: 66  KEAL-NGAEIMGQTIQVDWC 84

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 48.2 bits (114), Expect = 9e-08
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
             L++ +++  + ED I+  F   G I                  S GY  V++ T +  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEI-----KNIHLNLDRRTGFSKGYALVEYETHKQA 62

Query: 641 NQALKVLQNSSLDEHQIELKRS 662
             A + L  + +    I++   
Sbjct: 63  LAAKEALNGAEIMGQTIQVDWC 84

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFN 501
            I+ V ++       +++  F  +G++  + +             LVE+    QA AA  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 502 SLAYTKFKEVPLYLEWA 518
           +L   +     + ++W 
Sbjct: 68  ALNGAEIMGQTIQVDWC 84

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 8e-12
 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 7/90 (7%)

Query: 331 EDIAESGR-IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
           ED   S + ++VRNL  + +E+ + K F    P         +   K + +A V F   E
Sbjct: 2   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNRE 55

Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
            A +A + L+G V  G  + +   KP + +
Sbjct: 56  DAVEAMKALNGKVLDGSPIEVTLAKPVDKD 85

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 4e-07
 Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           +E        LY++NL  +++E+ I + F    P A   V + +D           Y FV
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-----------YAFV 49

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRS 662
            F  RE   +A+K L    LD   IE+  +
Sbjct: 50  HFSNREDAVEAMKALNGKVLDGSPIEVTLA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 8/83 (9%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + VRN+     +  +E+ F         R+ K        R + FV F  + +A  AMK
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVEAMK 62

Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
           AL     L G  + +  A+  D 
Sbjct: 63  AL-NGKVLDGSPIEVTLAKPVDK 84

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 5e-04
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 5/66 (7%)

Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
             ++E ++ +F         ++K     K R +AF+ +   + A  A+   N   +  S
Sbjct: 18 LSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKALNGKVLDGS 72

Query: 87 RIKVEK 92
           I+V  
Sbjct: 73 PIEVTL 78

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 8e-04
 Identities = 14/71 (19%), Positives = 23/71 (32%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
           +I+ V+NL   T    ++  F          V        V F  +  A  A  +L    
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 508 FKEVPLYLEWA 518
               P+ +  A
Sbjct: 69  LDGSPIEVTLA 79

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 1e-11
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++F+  LS+  T+ DL   F K+G + +  L +D  T +++GF  V F   E   +    
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD- 59

Query: 398 LDGTVFLGRML 408
                  G+++
Sbjct: 60  QKEHKLNGKVI 70

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 3e-09
 Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           ++I  L++++T+  ++ +F K G +   T+             S G+GFV F   ES+++
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPIT-----GRSRGFGFVLFKESESVDK 56

Query: 643 ALKVLQNSSLDEHQIELKR 661
            +   +   L+   I+ KR
Sbjct: 57  VMD-QKEHKLNGKVIDPKR 74

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 6e-07
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ +  + +   + ++++ F  FGE+    L    + +G  RGFGFV F       + M 
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI-TGRSRGFGFVLFKESESVDKVMD 59

Query: 747 ALCQSTHLYGRRL 759
              +   L G+ +
Sbjct: 60  Q--KEHKLNGKVI 70

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 8/71 (11%)

Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALNKN 278
           + +  L     KKDLK YF         T  L        G  ++ FK+ ++ +K +++ 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 279 KSFWKGKQLNI 289
           +    GK ++ 
Sbjct: 62  EHKLNGKVIDP 72

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.8 bits (142), Expect = 1e-11
 Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           +   +  R+FV NL   +TE+++ KLFEKYG   EV +  DK       F  +       
Sbjct: 3   KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTL 56

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           A  A   LD     G+ L +       +
Sbjct: 57  AEIAKVELDNMPLRGKQLRVRFACHSAS 84

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 11/92 (11%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
           E+     + L++ NL  + TE+ +R+ F+K G    V                 G+GF++
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-----------IHKDKGFGFIR 50

Query: 634 FYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
             TR     A   L N  L   Q+ ++ +  +
Sbjct: 51  LETRTLAEIAKVELDNMPLRGKQLRVRFACHS 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S++ V N+P    + E+ +LF+ +G           V     +GFGF+   T+  A+ A 
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYG-------KAGEVFIHKDKGFGFIRLETRTLAEIAK 61

Query: 746 KALCQSTHLYGRRLVLEWA 764
             L  +  L G++L + +A
Sbjct: 62  VEL-DNMPLRGKQLRVRFA 79

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 6e-08
 Identities = 16/72 (22%), Positives = 28/72 (38%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
           + V NLP      +++ LFE +G  G V +      G +    +  A+ A   L     +
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 70

Query: 510 EVPLYLEWAPEG 521
              L + +A   
Sbjct: 71  GKQLRVRFACHS 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 13/79 (16%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 223 QYHTIVVKNLPAGVKKKDLKAYFKPLP--LASVRTTFLGMAYIGFKDEKNCNKALNK-NK 279
           Q   + V NLP  + +++++  F+              G  +I  +       A  + + 
Sbjct: 7   QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDN 66

Query: 280 SFWKGKQLNIYKYSKDNSA 298
              +GKQL + +++  +++
Sbjct: 67  MPLRGKQLRV-RFACHSAS 84

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 2e-11
 Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-----IDKETDKTKGFALVTFLMPEHAT 392
           R++V N+ + +TE+ +   F     L  +        +  + ++ K FA + F   +  T
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKE 417
           QA    DG +F G+ L +   +P +
Sbjct: 63  QA-MAFDGIIFQGQSLKI--RRPHD 84

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 2e-10
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            LY+ N+ F  TE+++   F     +  +T A      +        + F++F + +   
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 642 QALKVLQNSSLDEHQIELKRSN 663
           QA+            ++++R +
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRPH 83

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 6/84 (7%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK----KMVGSGLHRGFGFVEFITKNEAK 742
           ++ V NIPF   +  + + F A   L  +          V     + F F+EF + +E  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 743 RAMKALCQSTHLYGRRLVLEWAEE 766
           +AM          G+ L +    +
Sbjct: 63  QAMA--FDGIIFQGQSLKIRRPHD 84

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 7/86 (8%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S  +FV   +  +TED+L + F +YG + +V           + FA VTF   + A    
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSLC 59

Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGN 421
              +  +  G  +H+   +PK N  +
Sbjct: 60  G--EDLIIKGISVHISNAEPKHNSNS 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 5e-08
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 9/84 (10%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S + V        + E+ E F  +G++  V +PK        R F FV F     A+   
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQIAQSLC 59

Query: 746 KALCQSTHLYGRRLVLEWAEEADN 769
               +   + G  + +  AE   N
Sbjct: 60  G---EDLIIKGISVHISNAEPKHN 80

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 10/82 (12%), Positives = 27/82 (32%), Gaps = 12/82 (14%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           + +++     + TED +R  F + G +  V +                + FV F   +  
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFI----------PKPFRAFAFVTFADDQIA 55

Query: 641 NQALKVLQNSSLDEHQIELKRS 662
                  ++  +    + +  +
Sbjct: 56  QSLCG--EDLIIKGISVHISNA 75

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 3e-11
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++++ NLS  VT DDL +LF           P+  +     G+A V +     A +A + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 398 LDGTVFL-GRMLHLIPGKPKEN 418
           L G V L G+++ +     K+ 
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKL 78

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 14/80 (17%), Positives = 36/80 (45%), Gaps = 7/80 (8%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           +K+ + N+       ++ +LF         ++           G+ FV++  +N A RA+
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAI 54

Query: 746 KALCQSTHLYGRRLVLEWAE 765
           + L     L+G+ + ++++ 
Sbjct: 55  ETLSGKVELHGKIMEVDYSV 74

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 12/82 (14%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            LYI NL+   T D +R+ F       +  V  K            GY FV +  +    
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----------GYAFVDYPDQNWAI 51

Query: 642 QALKVLQNS-SLDEHQIELKRS 662
           +A++ L     L    +E+  S
Sbjct: 52  RAIETLSGKVELHGKIMEVDYS 73

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 3e-11
 Identities = 25/82 (30%), Positives = 42/82 (51%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           +  ++++NLS  VTE DL  LF ++       +     T + +G A +TF   E A QA 
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
             ++G    G++L +  GK K+
Sbjct: 78  HLVNGYKLYGKILVIEFGKNKK 99

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 6e-07
 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 5/87 (5%)

Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
           EP+  LY+KNL+   TE  +   F +        +  +            G  F+ F  +
Sbjct: 16  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-----TGRMRGQAFITFPNK 70

Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNR 664
           E   QAL ++    L    + ++    
Sbjct: 71  EIAWQALHLVNGYKLYGKILVIEFGKN 97

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 0.001
 Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 2/94 (2%)

Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
             SS    +    + ++N+  +  + ++  LF  F E K   +  +M+ +G  RG  F+ 
Sbjct: 8   MFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-TGRMRGQAFIT 66

Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD 768
           F  K  A +A+  +     LYG+ LV+E+ +   
Sbjct: 67  FPNKEIAWQALHLV-NGYKLYGKILVIEFGKNKK 99

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 4e-11
 Identities = 28/87 (32%), Positives = 47/87 (54%), Gaps = 6/87 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +EPE    L+I  L+F +T++S+R HF++ G +    V R  + K      S G+GFV +
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKR-----SRGFGFVTY 55

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKR 661
            T E ++ A+   +   +D   +E KR
Sbjct: 56  ATVEEVDAAMN-ARPHKVDGRVVEPKR 81

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 9e-11
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           ++F+  LS+  T++ L   FE++G L + ++  D  T +++GF  VT+   E    A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 398 LDGTVFLGRML 408
                  GR++
Sbjct: 67  ARPHKVDGRVV 77

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 8e-08
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           K+ +  + F+     +   F+ +G L       +   +   RGFGFV + T  E   AM 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 747 ALCQSTHLYGRRLVLEWA 764
           A  +   + GR +  + A
Sbjct: 67  A--RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 7e-04
 Identities = 9/82 (10%), Positives = 25/82 (30%), Gaps = 11/82 (13%)

Query: 216 KAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGM--------AYIGFKD 267
           K P   R    + +  L      + L+++F+     +                 ++ +  
Sbjct: 1   KEPEQLR---KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 57

Query: 268 EKNCNKALNKNKSFWKGKQLNI 289
            +  + A+N       G+ +  
Sbjct: 58  VEEVDAAMNARPHKVDGRVVEP 79

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 5e-11
 Identities = 21/84 (25%), Positives = 41/84 (48%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           E   +F+ +L     + DL ++F  +G +    + IDK+T+ +K F  V++  P  A  A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 395 YQHLDGTVFLGRMLHLIPGKPKEN 418
            Q ++G     + L +   + K +
Sbjct: 77  IQSMNGFQIGMKRLKVQLKRSKND 100

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 5/95 (5%)

Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
           ++E      L+I +L     +  + + F   G + S  V   K        LS  +GFV 
Sbjct: 12  QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN-----LSKCFGFVS 66

Query: 634 FYTRESLNQALKVLQNSSLDEHQIELKRSNRNLES 668
           +    S   A++ +    +   +++++      +S
Sbjct: 67  YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 14/85 (16%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
           G+ + + ++P +    ++ ++F  FG             + L + FGFV +     A+ A
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGN-VVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 745 MKALCQSTHLYGRRLVLEWAEEADN 769
           ++++     +  +RL ++     ++
Sbjct: 77  IQSM-NGFQIGMKRLKVQLKRSKND 100

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.1 bits (137), Expect = 6e-11
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFE---KYGPLAEVILPIDKETDKT---KGFALVTFL 386
           + +   +FV  LS  + + ++ K  E   K+G + +V++        +      A VT++
Sbjct: 5   VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 64

Query: 387 MPEHATQAYQHLDGTVFLGRML 408
             E A +A Q ++  V  GR L
Sbjct: 65  RSEDALRAIQCVNNVVVDGRTL 86

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (100), Expect = 7e-06
 Identities = 9/77 (11%), Positives = 26/77 (33%), Gaps = 1/77 (1%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVT-VARKKDPKSPGQFLSMGYGFVQFYTRESL 640
            +++  L+    +  + +  +  G    +  V         G        +V +   E  
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 641 NQALKVLQNSSLDEHQI 657
            +A++ + N  +D   +
Sbjct: 70  LRAIQCVNNVVVDGRTL 86

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.2 bits (80), Expect = 0.004
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 678 SNVAKQTGSKILVRNIPFQAKQSEV---EELFKAFGELKFVRLP--KKMVGSGLHRGFGF 732
           ++V     + + V  +  +    EV    E F  FG++  V +       GS       +
Sbjct: 1   ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAY 60

Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRL 759
           V +I   +A RA++ +  +  + GR L
Sbjct: 61  VTYIRSEDALRAIQCV-NNVVVDGRTL 86

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 9e-11
 Identities = 26/85 (30%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           RI V NL Y VT D L ++F K+G + ++I          +  AL+ +  P  A  A   
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADPVSAQHAKLS 64

Query: 398 LDGTVFLGRMLHLIPGKPKENEGNV 422
           LDG         L     K    NV
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNV 89

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 3e-08
 Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 9/84 (10%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
             P   + ++NL +  T D + + F K G +  +    K          +     +Q+  
Sbjct: 4   QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---------NQFQALLQYAD 54

Query: 637 RESLNQALKVLQNSSLDEHQIELK 660
             S   A   L   ++      L+
Sbjct: 55  PVSAQHAKLSLDGQNIYNACCTLR 78

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (104), Expect = 4e-06
 Identities = 15/96 (15%), Positives = 41/96 (42%), Gaps = 7/96 (7%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           +I+V N+ +      + ++F  FG +  +    K      ++    +++     A+ A  
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKL 63

Query: 747 ALC-QSTHLYGRRLVLEWAEEAD-NVEDIRKRTNRY 780
           +L  Q+ +     L +++++    NV+    ++  Y
Sbjct: 64  SLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDY 99

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IFV  LS    E+ + + F  +G +  + LP+D +T+K +GF  +TF   E   +  + 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59

Query: 398 LDGTVFLGRML 408
                      
Sbjct: 60  KKYHNVGLSKC 70

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.0 bits (127), Expect = 1e-09
 Identities = 13/79 (16%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++  L+ ++ E+ IR +F   G +        + P         G+ F+ F   E + +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEV-----ESIELPMDNKTNKRRGFCFITFKEEEPVKK 56

Query: 643 ALKVLQNSSLDEHQIELKR 661
            ++  +  ++   + E+K 
Sbjct: 57  IME-KKYHNVGLSKCEIKV 74

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.2 bits (117), Expect = 3e-08
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           KI V  +     + ++ E F  FGE++ +        +   RGF F+ F  +   K+ M+
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIE-LPMDNKTNKRRGFCFITFKEEEPVKKIME 59

Query: 747 ALCQSTHLYGRRLVLEWA 764
              +  ++   +  ++ A
Sbjct: 60  K--KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 12/71 (16%), Positives = 22/71 (30%), Gaps = 8/71 (11%)

Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGM--------AYIGFKDEKNCNKALNKN 278
           I V  L     ++ ++ YF            +           +I FK+E+   K + K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 279 KSFWKGKQLNI 289
                  +  I
Sbjct: 62  YHNVGLSKCEI 72

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 1e-10
 Identities = 22/70 (31%), Positives = 34/70 (48%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           +++R L    T+ DL KL + YG +      +DK T+K KG+  V F  P  A +A   L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 399 DGTVFLGRML 408
             +    +M 
Sbjct: 61  KASGVQAQMA 70

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 8e-05
 Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           LYI+ L   +T+  + +  +  G I S      K           GYGFV F +  +  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKC-----KGYGFVDFDSPSAAQK 55

Query: 643 ALKVLQNSSLDEHQI 657
           A+  L+ S +     
Sbjct: 56  AVTALKASGVQAQMA 70

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 12/72 (16%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           + +R +       ++ +L + +G+            +   +G+GFV+F + + A++A+ A
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGK-IVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 59

Query: 748 LCQSTHLYGRRL 759
           L +++ +  +  
Sbjct: 60  L-KASGVQAQMA 70

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 1e-10
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + ++       E+  T++ EKYG + E+ +  D   D   G   V F   E A +A   L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 399 DGTVFLGRMLH 409
           +   F G+ +H
Sbjct: 89  NNRWFNGQPIH 99

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 5e-07
 Identities = 14/96 (14%), Positives = 32/96 (33%), Gaps = 6/96 (6%)

Query: 567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
           +N  +  +      + + ++       E+      +K G +  + V              
Sbjct: 14  QNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDH------L 67

Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRS 662
           +G  +V+F   E   +A+  L N   +   I  + S
Sbjct: 68  VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 14/78 (17%), Positives = 31/78 (39%)

Query: 14  HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQA 73
             ++ D++  E   +  +E      E+ G V ++ +            ++ + RE+ A+ 
Sbjct: 24  RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEK 83

Query: 74  ALDYFNNTYVFSSRIKVE 91
           A+   NN +     I  E
Sbjct: 84  AVIDLNNRWFNGQPIHAE 101

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 12/83 (14%), Positives = 36/83 (43%), Gaps = 3/83 (3%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
            +   S + ++    +  +    E+ + +GE++ + +   +       G  +V+F  + +
Sbjct: 23  LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL--GDHLVGNVYVKFRREED 80

Query: 741 AKRAMKALCQSTHLYGRRLVLEW 763
           A++A+  L  +    G+ +  E 
Sbjct: 81  AEKAVIDL-NNRWFNGQPIHAEL 102

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.4 bits (135), Expect = 1e-10
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 6/94 (6%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
            D+ E   +F+RNLS+   E+ L ++ +++G L  V + +  +T+ +KG A   F+  E 
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 391 ATQAYQHL------DGTVFLGRMLHLIPGKPKEN 418
           A +            G    GR L +     ++ 
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.8 bits (105), Expect = 2e-06
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 11/99 (11%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           +     T++I+NL+F+S E+++    ++ G +  V V    D        S G  F QF 
Sbjct: 4   DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-----TEHSKGCAFAQFM 58

Query: 636 TRESLNQALKVLQNSS------LDEHQIELKRSNRNLES 668
           T+E+  + L      +      LD  Q+++  +    E+
Sbjct: 59  TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.7 bits (97), Expect = 2e-05
 Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 6/92 (6%)

Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
             G  + +RN+ F +++  + E+ + FG+LK+VR+          +G  F +F+T+  A+
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH-SKGCAFAQFMTQEAAQ 64

Query: 743 RAMKAL-----CQSTHLYGRRLVLEWAEEADN 769
           + + A           L GR+L ++ A   D 
Sbjct: 65  KCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.6 bits (133), Expect = 2e-10
 Identities = 14/78 (17%), Positives = 29/78 (37%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +++ N   + T+ ++  L +    +A  I       + ++ FA +     E A    + 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 398 LDGTVFLGRMLHLIPGKP 415
           L+G    G  L      P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.8 bits (118), Expect = 2e-08
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           + TL++ N   + T+ +IR   +    +     A      S     S  + ++   ++E 
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVV-----ALSIRLPSLRFNTSRRFAYIDVTSKED 55

Query: 640 LNQALKVLQNSSLDEHQIELKRSN 663
               ++ L    ++ + +  K SN
Sbjct: 56  ARYCVEKLNGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.2 bits (106), Expect = 9e-07
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + + N P    Q  + +L +    +         +     R F +++  +K +A+  ++
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSI-RLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 747 ALCQSTHLYGRRLVLEWAE 765
            L     + G  LV + + 
Sbjct: 62  KL-NGLKIEGYTLVTKVSN 79

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 3e-10
 Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 5/88 (5%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IFV  L Y  T+  L K FE +G + E ++  D++T K++G+  VT      A +A + 
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 398 LDGTVFLGRMLHL----IPGKPKENEGN 421
            +     GR  ++    +  KP+  +  
Sbjct: 72  PNPI-IDGRKANVNLAYLGAKPRSLQTG 98

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 6/90 (6%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           ++    T +++  L +++T+ S+R++F+  G I    V   +         S GYGFV  
Sbjct: 5   QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ-----TGKSRGYGFVTM 59

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNR 664
             R +  +A K   N  +D  +  +  +  
Sbjct: 60  ADRAAAERACKDP-NPIIDGRKANVNLAYL 88

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
            T +KI V  +P+    + + + F+ FG+++          +G  RG+GFV    +  A+
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAV-VITDRQTGKSRGYGFVTMADRAAAE 66

Query: 743 RAMKALCQSTHLYGRRLVLEWAEE 766
           RA K       + GR+  +  A  
Sbjct: 67  RACKDPNPI--IDGRKANVNLAYL 88

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 3e-10
 Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
             F+ NL Y VTE+ + + F      A  +       ++ KGF    F   +    +   
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL-LSALS 75

Query: 398 LDGTVFLGRMLHLIPGKPKENE 419
           L+      + + +      +++
Sbjct: 76  LNEESLGNKRIRVDVADQAQDK 97

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 4e-07
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 3/93 (3%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
            S + K       + N+P+   +  ++E F+       VRLP++       +GFG+ EF 
Sbjct: 7   GSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFE 65

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
             +    A+        L  +R+ ++ A++A +
Sbjct: 66  DLDSLLSALS--LNEESLGNKRIRVDVADQAQD 96

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 7e-07
 Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 6/92 (6%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
                 P  T ++ NL ++ TE+SI+  F+     A        +P+    F        
Sbjct: 8   SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYA----- 62

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
           +F   +SL  AL  L   SL   +I +  +++
Sbjct: 63  EFEDLDSLLSALS-LNEESLGNKRIRVDVADQ 93

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 4e-10
 Identities = 27/81 (33%), Positives = 42/81 (51%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
            +FV N+ Y  TE+ L  +F + GP+    L  D+ET K KG+    +   E A  A ++
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 398 LDGTVFLGRMLHLIPGKPKEN 418
           L+G  F GR L +     ++N
Sbjct: 70  LNGREFSGRALRVDNAASEKN 90

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 2/90 (2%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + V NIP++A + +++++F   G +   RL          +G+GF E+  +  A  AM+
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGK-PKGYGFCEYQDQETALSAMR 68

Query: 747 ALCQSTHLYGRRLVLEWAEEADNVEDIRKR 776
            L       GR L ++ A    N E+++  
Sbjct: 69  NL-NGREFSGRALRVDNAASEKNKEELKSL 97

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 16/97 (16%), Positives = 39/97 (40%), Gaps = 8/97 (8%)

Query: 576 EPEPD---TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           +P  D    ++++ N+ + +TE+ ++  F + GP+        +           GYGF 
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPV-----VSFRLVYDRETGKPKGYGFC 55

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESE 669
           ++  +E+   A++ L         + +  +      E
Sbjct: 56  EYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.9 bits (131), Expect = 5e-10
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
             + N+ +++T+ D+ +  E        +  +     +  G ALV F   + A ++ + L
Sbjct: 11  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-L 69

Query: 399 DGTVFLGRMLHLIPGKPKE 417
                 GR   +     ++
Sbjct: 70  HRKKLNGREAFVHVVTLED 88

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (102), Expect = 5e-06
 Identities = 12/98 (12%), Positives = 29/98 (29%), Gaps = 6/98 (6%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           E          +I N+ F+ T+  + +  +      +       +         +G   V
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ-----GLGQALV 55

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA 670
           QF   +   ++ + L    L+  +  +         E 
Sbjct: 56  QFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREI 92

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 0.002
 Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 3/90 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
              + NIPF   + +V +  +     +          +G   G   V+F  +++A+++ +
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSER 68

Query: 747 ALCQSTHLYGRRLVLEWAEEADNVEDIRKR 776
                  L GR   +      D  E  +  
Sbjct: 69  --LHRKKLNGREAFVHVVTLEDMREIEKNP 96

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.0 bits (129), Expect = 6e-10
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IFV  LS   T +D+   FE++G + + +L  DK T++ +GF  VTF   +   +  + 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 398 LDGTVFLGRMLH 409
           +       +M+ 
Sbjct: 60  IHFHEINNKMVE 71

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 12/79 (15%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
           +++  L+ N+T + ++ +F++ G +                    G+GFV F + + + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKV-----DDAMLMFDKTTNRHRGFGFVTFESEDIVEK 56

Query: 643 ALKVLQNSSLDEHQIELKR 661
             + +    ++   +E K+
Sbjct: 57  VCE-IHFHEINNKMVECKK 74

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.5 bits (107), Expect = 5e-07
 Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           KI V  +       +V+  F+ FG++           +  HRGFGFV F +++  ++  +
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAM-LMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

Query: 747 ALCQSTHLYGRRLVLEWA 764
                  +  + +  + A
Sbjct: 60  I--HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 11/71 (15%), Positives = 19/71 (26%), Gaps = 8/71 (11%)

Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGM--------AYIGFKDEKNCNKALNKN 278
           I V  L      +D+K YF+                       ++ F+ E    K    +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 279 KSFWKGKQLNI 289
                 K +  
Sbjct: 62  FHEINNKMVEC 72

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 8e-10
 Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 7/87 (8%)

Query: 336 SGRIFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
           +  I++ NL+  + +D+L K    +F ++G + ++++       K +G A V F     A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS---LKMRGQAFVIFKEVSSA 59

Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKEN 418
           T A + + G  F  + + +   K   +
Sbjct: 60  TNALRSMQGFPFYDKPMRIQYAKTDSD 86

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            I + N+  + K+ E+++   A        L   +  S   RG  FV F   + A  A++
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 747 ALCQSTHLYGRRLVLEWAEE 766
           ++ Q    Y + + +++A+ 
Sbjct: 65  SM-QGFPFYDKPMRIQYAKT 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 4e-08
 Identities = 21/104 (20%), Positives = 36/104 (34%), Gaps = 15/104 (14%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
           P+ T+YI NLN    +D +++              +  D          G  FV F    
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFS----RFGQILDILVSRSLKMRGQAFVIFKEVS 57

Query: 639 SLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAK 682
           S   AL+ +Q     +  + ++ +           K  S  +AK
Sbjct: 58  SATNALRSMQGFPFYDKPMRIQYA-----------KTDSDIIAK 90

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 1e-09
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +   ++V      +T   L   F  +G + ++ +   +        A VT+   E A QA
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQA 55

Query: 395 YQHLDGTVFLGRMLHLIPGKPK 416
              L+GT      L +   + +
Sbjct: 56  VAELNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 6e-08
 Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 13/88 (14%)

Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
           P    TLY+   +   T   +R  F   G I  ++                   FV +  
Sbjct: 2   PRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLS-----------MDPPRNCAFVTYEK 48

Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNR 664
            ES +QA+  L  + ++  Q+++  + +
Sbjct: 49  MESADQAVAELNGTQVESVQLKVNIARK 76

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 7e-05
 Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 10/86 (11%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
           A + G+ + V         + +   F  FG           +     R   FV +     
Sbjct: 1   APRKGNTLYVYGED--MTPTLLRGAFSPFG-------NIIDLSMDPPRNCAFVTYEKMES 51

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEE 766
           A +A+  L   T +   +L +  A +
Sbjct: 52  ADQAVAEL-NGTQVESVQLKVNIARK 76

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 54.9 bits (131), Expect = 1e-09
 Identities = 29/123 (23%), Positives = 48/123 (39%)

Query: 304 ADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPL 363
            D     +      +  +      Q   +      + V  +  TV E  L +LFE+YGP+
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69

Query: 364 AEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVD 423
             V +  D+ET +++G+  V F     A QA   L+G   L + L +           + 
Sbjct: 70  ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA 129

Query: 424 GKV 426
           G V
Sbjct: 130 GAV 132

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 46.8 bits (110), Expect = 1e-06
 Identities = 23/128 (17%), Positives = 44/128 (34%), Gaps = 5/128 (3%)

Query: 552 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 611
               +  Q    + +         EP+    L +  +     E  +R+ F++ GPI    
Sbjct: 14  GQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI---- 69

Query: 612 VARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEAT 671
               K         S GYGFV+F +  S  QA+  L   ++   ++++  +    +    
Sbjct: 70  -ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGI 128

Query: 672 TVKRKSSN 679
                  N
Sbjct: 129 AGAVGDGN 136

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 42.6 bits (99), Expect = 3e-05
 Identities = 19/106 (17%), Positives = 44/106 (41%), Gaps = 2/106 (1%)

Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
           +  +  + +   +     N        ++V  IP    + ++ +LF+ +G          
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGP-IESVKIVC 76

Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
              +   RG+GFV+F + + A++A+  L    ++  +RL +  A  
Sbjct: 77  DRETRQSRGYGFVKFQSGSSAQQAIAGL-NGFNILNKRLKVALAAS 121

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 1/72 (1%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           +IFV  +     E  L   FE+YG +  + +  D+ + K +GFA VTF   + +      
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVI 62

Query: 398 LDGTVFLGRMLH 409
                  G    
Sbjct: 63  QKYHTVNGHNCE 74

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 12/81 (14%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
            +++  +  ++ E  +R +F++ G I  + +   +           G+ FV F   +S++
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS-----GKKRGFAFVTFDDHDSVD 58

Query: 642 QALKVLQNSSLDEHQIELKRS 662
           + +   +  +++ H  E++++
Sbjct: 59  KIVI-QKYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 0.002
 Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 3/78 (3%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
           KI V  I    ++  + + F+ +G+++ + +          RGF FV F   +   + + 
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK-KRGFAFVTFDDHDSVDKIVI 62

Query: 747 ALCQSTHLYGRRLVLEWA 764
              +   + G    +  A
Sbjct: 63  --QKYHTVNGHNCEVRKA 78

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.9 bits (121), Expect = 9e-09
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 335 ESGRIFVRNLSYTVT-EDDLTKLFEKY-GPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
           E   I +RNLS  +  E+ L + FE +       I    KE       A + F   + A 
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 393 QAYQHLDGTVFLGRMLHLIPGKPK 416
           +A Q ++ ++   R + +     K
Sbjct: 63  RALQ-MNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.8 bits (100), Expect = 8e-06
 Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 3/82 (3%)

Query: 685 GSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
           G +I++RN+  +   ++ + E F+ FG ++ + +P        +    F+ F  K+ A+R
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 744 AMKALCQSTHLYGRRLVLEWAE 765
           A++     + L  R + +  A+
Sbjct: 64  ALQM--NRSLLGNREISVSLAD 83

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.6 bits (89), Expect = 2e-04
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 6/85 (7%)

Query: 581 TTLYIKNLNFNST-EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
             + I+NL+     E+ +R  F+  G I                  +    F+ F  ++S
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSI----EKINIPAGQKEHSFNNCCAFMVFENKDS 60

Query: 640 LNQALKVLQNSSLDEHQIELKRSNR 664
             +AL+ +  S L   +I +  +++
Sbjct: 61  AERALQ-MNRSLLGNREISVSLADK 84

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 20/81 (24%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S  I V+NL       ++  L + Y              D+ K  A VT L  E A  A 
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 396 QHLDGTVFLGRMLHLIPGKPK 416
           Q      F G+ L +      
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTD 78

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           S ILV+N+P  +   EV +L K +          K      ++   FV  +   +A+ A+
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD--------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 746 KALCQSTHLYGRRLVLEWAE 765
           +         G+ L+++   
Sbjct: 58  QMF-HQYSFRGKDLIVQLQP 76

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 11/85 (12%), Positives = 24/85 (28%), Gaps = 12/85 (14%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           + + +KNL  +S    +    K                K      +    FV     E  
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD------------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 641 NQALKVLQNSSLDEHQIELKRSNRN 665
             A+++    S     + ++    +
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTD 78

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 6e-05
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 1/70 (1%)

Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
           ILVKNLP  +   ++  L + +      +         V  L   QA+ A        F+
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAF-VTLLNGEQAQNAIQMFHQYSFR 66

Query: 510 EVPLYLEWAP 519
              L ++  P
Sbjct: 67  GKDLIVQLQP 76

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.7 bits (118), Expect = 3e-08
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 8/87 (9%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           + R++V  L    +   L + F+++G +  +         K   FA + +   + A  A 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTID------HVKGDSFAYIQYESLDAAQAAC 70

Query: 396 QHLDGTVFLGRMLHLI--PGKPKENEG 420
             + G    G    L     K   + G
Sbjct: 71  AKMRGFPLGGPDRRLRVDFAKSGPSSG 97

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 11/85 (12%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           +  P T L++  L  N++  ++ R F + G I ++                  + ++Q+ 
Sbjct: 13  KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID-----------HVKGDSFAYIQYE 61

Query: 636 TRESLNQALKVLQNSSLDEHQIELK 660
           + ++   A   ++   L      L+
Sbjct: 62  SLDAAQAACAKMRGFPLGGPDRRLR 86

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 13/82 (15%), Positives = 34/82 (41%), Gaps = 10/82 (12%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           +++ V  +      + +   F  FG         + +       F ++++ + + A+ A 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFG-------SIRTIDHVKGDSFAYIQYESLDAAQAAC 70

Query: 746 KALCQSTHLYG--RRLVLEWAE 765
             + +   L G  RRL +++A+
Sbjct: 71  AKM-RGFPLGGPDRRLRVDFAK 91

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
             + V  L   T    L   F+ FG +  +          +++   + A+AA   +    
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 508 F--KEVPLYLEWA 518
               +  L +++A
Sbjct: 78  LGGPDRRLRVDFA 90

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (117), Expect = 4e-08
 Identities = 15/84 (17%), Positives = 26/84 (30%), Gaps = 7/84 (8%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V  L  + +  DL     + G        +     +  G  +V +L  E    A + 
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAG-------DVCYADVQKDGMGMVEYLRKEDMEYALRK 69

Query: 398 LDGTVFLGRMLHLIPGKPKENEGN 421
           LD T F          +      +
Sbjct: 70  LDDTKFRSHEGETSYIRVYPERSS 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 12/90 (13%), Positives = 28/90 (31%), Gaps = 12/90 (13%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
                D  + +  L  + +   ++ H ++                        G G V++
Sbjct: 10  PTRRSDFRVLVSGLPPSGSWQDLKDHMREA------------GDVCYADVQKDGMGMVEY 57

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNR 664
             +E +  AL+ L ++    H+ E      
Sbjct: 58  LRKEDMEYALRKLDDTKFRSHEGETSYIRV 87

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.5 bits (99), Expect = 1e-05
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 3/90 (3%)

Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYF-KPLPLASVRTTFLGMAYIGFKDEKNCNK 273
           S  P  +R    ++V  LP     +DLK +  +   +        GM  + +  +++   
Sbjct: 6   SGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEY 65

Query: 274 ALNK-NKSFWKGKQLNIYKYSKDNSAKYSG 302
           AL K + + ++  +     Y +    + SG
Sbjct: 66  ALRKLDDTKFRSHEGET-SYIRVYPERSSG 94

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.0 bits (90), Expect = 2e-04
 Identities = 11/86 (12%), Positives = 29/86 (33%), Gaps = 9/86 (10%)

Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
            +++  ++LV  +P      ++++  +                     G G VE++ K +
Sbjct: 11  TRRSDFRVLVSGLPPSGSWQDLKDHMREA--------GDVCYADVQKDGMGMVEYLRKED 62

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEE 766
            + A++ L   T          +   
Sbjct: 63  MEYALRKL-DDTKFRSHEGETSYIRV 87

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 5e-08
 Identities = 19/83 (22%), Positives = 27/83 (32%), Gaps = 3/83 (3%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + +R L Y  TE+D+   F    P+            +  G A V F   E A  A    
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVH--IEIGPDGRVTGEADVEFATHEDAVAAMA-K 74

Query: 399 DGTVFLGRMLHLIPGKPKENEGN 421
           D      R + L         G+
Sbjct: 75  DKANMQHRYVELFLNSTAGTSGS 97

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 4e-07
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 5/93 (5%)

Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
            S+    TG  + +R +P++A ++++   F     ++           G   G   VEF 
Sbjct: 7   GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD---GRVTGEADVEFA 63

Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
           T  +A  AM       ++  R + L     A  
Sbjct: 64  THEDAVAAMA--KDKANMQHRYVELFLNSTAGT 94

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 5e-07
 Identities = 13/89 (14%), Positives = 31/89 (34%), Gaps = 8/89 (8%)

Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
           +      ++++ L + +TE+ I   F    P+            +           V+F 
Sbjct: 11  QSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG-------EADVEFA 63

Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNR 664
           T E    A+     +++    +EL  ++ 
Sbjct: 64  THEDAVAAMA-KDKANMQHRYVELFLNST 91

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 14/91 (15%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKP------LPLASVRTTFLGMAYIGFKDE 268
           S +       H + ++ LP    + D+  +F P                 G A + F   
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATH 65

Query: 269 KNCNKALNKNKSFWKGKQLNIYKYSKDNSAK 299
           ++   A+ K+K+  + + + ++  S   ++ 
Sbjct: 66  EDAVAAMAKDKANMQHRYVELFLNSTAGTSG 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 7e-08
 Identities = 14/96 (14%), Positives = 33/96 (34%), Gaps = 2/96 (2%)

Query: 321 KSQEDSVQFA-EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG 379
           K+     Q A +   +   +++ NL  ++ E +L  + + +G +      +   +  ++G
Sbjct: 2   KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-ILRDSSGTSRG 60

Query: 380 FALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKP 415
                    E       H +G           P +P
Sbjct: 61  VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 3e-04
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 9/89 (10%)

Query: 565 VEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 624
           V+  + + +E++P   T LYI NL  +  E  +    K  G + S  + R          
Sbjct: 6   VQAQMAKQQEQDP---TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT----- 57

Query: 625 LSMGYGFVQFYTRESLNQALKVLQNSSLD 653
            S G GF +  + E     +       + 
Sbjct: 58  -SRGVGFARMESTEKCEAVIGHFNGKFIK 85

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.0 bits (116), Expect = 7e-08
 Identities = 16/87 (18%), Positives = 24/87 (27%), Gaps = 11/87 (12%)

Query: 336 SGRIFVRNLSYTVTEDDLTK-----LFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           S  +     +  V  +  T+     LF  Y                      + F  P  
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLS 58

Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKE 417
           A  A   L  T FLG+ + L   +   
Sbjct: 59  AADARLRLHKTEFLGKEMKLYFAQTLH 85

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 3e-06
 Identities = 9/92 (9%), Positives = 20/92 (21%), Gaps = 16/92 (17%)

Query: 578 EPDTTLYIKNLNF-----NSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
              + L     N      + T       F+      +    +                 +
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----------KRVRI 51

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
            F    S   A   L  +     +++L  +  
Sbjct: 52  NFSNPLSAADARLRLHKTEFLGKEMKLYFAQT 83

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 5e-06
 Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 13/85 (15%)

Query: 686 SKILVRNIPF-----QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
           S ++              +++ E LF+ + +    +  K             + F     
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-------SFKRVRINFSNPLS 58

Query: 741 AKRAMKALCQSTHLYGRRLVLEWAE 765
           A  A   L + T   G+ + L +A+
Sbjct: 59  AADARLRLHK-TEFLGKEMKLYFAQ 82

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 0.002
 Identities = 10/74 (13%), Positives = 19/74 (25%), Gaps = 5/74 (6%)

Query: 450 ILVKNLP-----YRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
           ++                  ++LF  +                + F     A  A   L 
Sbjct: 8   LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLH 67

Query: 505 YTKFKEVPLYLEWA 518
            T+F    + L +A
Sbjct: 68  KTEFLGKEMKLYFA 81

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 46.4 bits (109), Expect = 3e-07
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
           TT+ +KNL  +  ++ + ++FK CGPI  V VA               +  ++F   +  
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-------FARIEFARYDGA 53

Query: 641 NQALKVLQNSSLDEHQIELKR 661
             A+    +  + +++I +  
Sbjct: 54  LAAITK-THKVVGQNEIIVSH 73

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.6 bits (94), Expect = 3e-05
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 5/79 (6%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + +LV+N+P    Q++V + FK  G +  V +   +     +  F  +EF   + A  A+
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK---NFRFARIEFARYDGALAAI 57

Query: 746 KALCQSTHLYGRRLVLEWA 764
                   +    +++   
Sbjct: 58  T--KTHKVVGQNEIIVSHL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.2 bits (93), Expect = 4e-05
 Identities = 10/71 (14%), Positives = 22/71 (30%), Gaps = 3/71 (4%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + V+NL  +  ++ + K F+  GP+  V +    + +                  A    
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFAR---IEFARYDGALAAITK 59

Query: 399 DGTVFLGRMLH 409
              V     + 
Sbjct: 60  THKVVGQNEII 70

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 4e-07
 Identities = 20/76 (26%), Positives = 29/76 (38%), Gaps = 4/76 (5%)

Query: 343 NLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTV 402
            L      +DL     K+G + +++L          G A V+F  PE A    Q LDG  
Sbjct: 26  PLVLNEIREDLRVECSKFGQIRKLLLF----DRHPDGVASVSFRDPEEADYCIQTLDGRW 81

Query: 403 FLGRMLHLIPGKPKEN 418
           F GR +         +
Sbjct: 82  FGGRQITAQAWDGTTD 97

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 9/83 (10%), Positives = 31/83 (37%), Gaps = 3/83 (3%)

Query: 9  VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHRE 68
          V+ +N    +D ++   +    +E L+ +  + G +  +      +      A + +   
Sbjct: 11 VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKL---LLFDRHPDGVASVSFRDP 67

Query: 69 DQAQAALDYFNNTYVFSSRIKVE 91
          ++A   +   +  +    +I  +
Sbjct: 68 EEADYCIQTLDGRWFGGRQITAQ 90

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 11/62 (17%), Positives = 19/62 (30%), Gaps = 3/62 (4%)

Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
           E+L     +   +R            G   V F    EA   ++ L       GR++  +
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRH--PDGVASVSFRDPEEADYCIQTL-DGRWFGGRQITAQ 90

Query: 763 WA 764
             
Sbjct: 91  AW 92

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 15/93 (16%), Positives = 26/93 (27%), Gaps = 20/93 (21%)

Query: 577 PEPDTTLYIKNL-----------NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
              +  + IKN+             N   + +R    K G I  + +  +          
Sbjct: 5   MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPD------- 57

Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDEHQIE 658
             G   V F   E  +  ++ L        QI 
Sbjct: 58  --GVASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (107), Expect = 7e-07
 Identities = 17/88 (19%), Positives = 27/88 (30%), Gaps = 7/88 (7%)

Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           R+ V  L  + +  DL     + G        +        G  +V F+  E  T A + 
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAG-------DVCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGK 425
           LD T F          + K +       
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSY 82

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (109), Expect = 8e-07
 Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 2/69 (2%)

Query: 343 NLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
           +  Y    +D+     KYG +   E+  P+D       G   V F       +A Q L G
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 401 TVFLGRMLH 409
             F  R++ 
Sbjct: 81  RKFANRVVV 89

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 689 LVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG-SGLHRGFGFVEFITKNEAKRAMKA 747
           L+ +  ++    +V +    +G +K + +P+ + G      G  FVEF +  + ++AM+ 
Sbjct: 18  LLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG 77

Query: 748 LCQSTHLYGRRLVLEWAEEAD 768
           L        R +V ++ +   
Sbjct: 78  L-TGRKFANRVVVTKYCDPDS 97

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 17/96 (17%), Positives = 37/96 (38%), Gaps = 6/96 (6%)

Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK 376
           AKH   + + ++      +S  +    L   V+ + L  + EK G +  ++         
Sbjct: 1   AKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL------MPP 54

Query: 377 TKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP 412
            K ++   +   E + +AY  L+G   +  +   I 
Sbjct: 55  NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT 90

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 13/89 (14%), Positives = 28/89 (31%), Gaps = 13/89 (14%)

Query: 570 EEDEEREPEPDTTLYIK--NLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 627
            E  E       +L +    L    + + +    +KCG + ++               + 
Sbjct: 8   HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-----------MPPNK 56

Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDEHQ 656
            Y F ++ T E   +A   L    + +  
Sbjct: 57  PYSFARYRTTEESKRAYVTLNGKEVVDDL 85

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 5/90 (5%)

Query: 434 KLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQK 493
           + +    V  A    ++    L        L  + E  G +  +L+PP        +   
Sbjct: 7   RHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTT 66

Query: 494 NQAKAAFNSLAYTKFKE-----VPLYLEWA 518
            ++K A+ +L   +  +     + LYL + 
Sbjct: 67  EESKRAYVTLNGKEVVDDLGQKITLYLNFV 96

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 45.3 bits (106), Expect = 1e-06
 Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 2/82 (2%)

Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
               +F+ NL+   +  +L     +       +  +D  T   + F  V F   E   +A
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEKA 70

Query: 395 YQHLDGTVFLGRMLHLIPGKPK 416
              L G    G  + L   K +
Sbjct: 71  L-ELTGLKVFGNEIKLEKPKGR 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 41.5 bits (96), Expect = 2e-05
 Identities = 19/90 (21%), Positives = 38/90 (42%), Gaps = 7/90 (7%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
           E  E      L+I NLN N +   ++    +      + V   +         +  +G+V
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT------NRKFGYV 59

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRS 662
            F + E L +AL+ L    +  ++I+L++ 
Sbjct: 60  DFESAEDLEKALE-LTGLKVFGNEIKLEKP 88

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (107), Expect = 1e-06
 Identities = 24/106 (22%), Positives = 44/106 (41%), Gaps = 3/106 (2%)

Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
           KR  S    + G  + ++ +PF+A+   V + FK    ++          +G   G GFV
Sbjct: 7   KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEGFV 65

Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
           EF  + + K A+    Q  ++  R + +    +   +E I     R
Sbjct: 66  EFRNEADYKAALCRHKQ--YMGNRFIQVHPITKKGMLEKIDMIRKR 109

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (88), Expect = 4e-04
 Identities = 18/107 (16%), Positives = 29/107 (27%), Gaps = 6/107 (5%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
                E    +Y+K L F +    +   FKK   +                      GFV
Sbjct: 11  SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE-----GFV 65

Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN 679
           +F        AL       +    I++    +    E   + RK   
Sbjct: 66  EFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQ 111

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 336 SGRIFVRNLS-YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
           +  + V NL+   VT   L  LF  YG +  V +  +K+       ALV       A  A
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLA 56

Query: 395 YQHLDGTVFLGRMLHLIPGKPKE 417
             HL+G    G+ + +   K + 
Sbjct: 57  MSHLNGHKLHGKPIRITLSKHQN 79

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 7e-05
 Identities = 17/86 (19%), Positives = 24/86 (27%), Gaps = 11/86 (12%)

Query: 581 TTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           + L + NLN    T  S+   F   G +  V +           F       VQ      
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI----------LFNKKENALVQMADGNQ 52

Query: 640 LNQALKVLQNSSLDEHQIELKRSNRN 665
              A+  L    L    I +  S   
Sbjct: 53  AQLAMSHLNGHKLHGKPIRITLSKHQ 78

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.2 bits (101), Expect = 8e-06
 Identities = 11/94 (11%), Positives = 26/94 (27%), Gaps = 13/94 (13%)

Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
              +      ++++ L  +  E  +    +K G I  V +                   V
Sbjct: 8   SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----------KRQALV 56

Query: 633 QFYTRESLNQALKVLQNS--SLDEHQIELKRSNR 664
           +F   +S  + +    +    +   Q     S  
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS 90

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (100), Expect = 9e-06
 Identities = 20/90 (22%), Positives = 32/90 (35%), Gaps = 8/90 (8%)

Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
              ++ S  + VR L  +V E DL +  EK+G +  V++   K        ALV F   +
Sbjct: 9   HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENID 62

Query: 390 HATQAYQHLD--GTVFLGRMLHLIPGKPKE 417
            A +             G+         K 
Sbjct: 63  SAKECVTFAADVPVYIAGQQAFFNYSTSKR 92

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.2 bits (93), Expect = 9e-05
 Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 9/90 (10%)

Query: 677 SSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
           S +  K + S ++ VR +     ++++ E  + FG + +V +          +    VEF
Sbjct: 6   SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-------FKRQALVEF 58

Query: 736 ITKNEAKRAMKAL-CQSTHLYGRRLVLEWA 764
              + AK  +        ++ G++    ++
Sbjct: 59  ENIDSAKECVTFAADVPVYIAGQQAFFNYS 88

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.4 bits (91), Expect = 2e-04
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
            ++ V+ L    +  DL    E FG +  V++ P+    LVEF   + AK      A   
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 508 F--KEVPLYLEWA 518
                   +  ++
Sbjct: 76  VYIAGQQAFFNYS 88

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
           S  + + N+  +V+E+DL  LF   G     ++   K   K +  AL+     E A QA 
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRKMALIQMGSVEEAVQAL 65

Query: 396 QHLDGTVFL-GRMLHLIPGKPK 416
             L          L +   K  
Sbjct: 66  IDLHNHDLGENHHLRVSFSKST 87

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 6e-05
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
           + + + NIP    + +++ LF + G +       +       R    ++  +  EA +A+
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQAL 65

Query: 746 KALCQSTHLYGRRLVLEWA 764
             L          L + ++
Sbjct: 66  IDLHNHDLGENHHLRVSFS 84

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 9e-05
 Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 9/76 (11%)

Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
           P  TL++ N+  + +E+ ++  F   G +                        +Q  + E
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVV---------KGFKFFQKDRKMALIQMGSVE 59

Query: 639 SLNQALKVLQNSSLDE 654
              QAL  L N  L E
Sbjct: 60  EAVQALIDLHNHDLGE 75

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 14/80 (17%), Positives = 25/80 (31%), Gaps = 9/80 (11%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           + V           L   F +YG + +           T  +  + +     A +A    
Sbjct: 7   VTVFGFPQASASYIL-LQFAQYGNILKH------VMSNTGNWMHIRYQSKLQARKALS-K 58

Query: 399 DGTVFLGR-MLHLIPGKPKE 417
           DG +F    M+ + P   K 
Sbjct: 59  DGRIFGESIMIGVKPCIDKN 78

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 4e-05
 Identities = 10/78 (12%), Positives = 23/78 (29%), Gaps = 13/78 (16%)

Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
           DT + +      S    I   F + G I    ++               +  +++ ++  
Sbjct: 4   DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSNTG-----------NWMHIRYQSKLQ 51

Query: 640 LNQALKVLQNSSLDEHQI 657
             +AL         E  +
Sbjct: 52  ARKALS-KDGRIFGESIM 68

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 5e-05
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 2/79 (2%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
           ++  ++  ++++      T DD+ +  E  G +  +           KG   V F   E 
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIES 59

Query: 391 ATQAYQHLDGTVFLGRMLH 409
           A +  +   G  +    L 
Sbjct: 60  AKKFVE-TPGQKYKETDLL 77

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 9e-05
 Identities = 11/80 (13%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
            + ++  P  A   +++E  +  G++  +++ + +  +   +G  FV F +   AK+ ++
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA--FKGSIFVVFDSIESAKKFVE 65

Query: 747 ALCQSTHLYGRRLVLEWAEE 766
                       L++ + ++
Sbjct: 66  T--PGQKYKETDLLILFKDD 83

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 2e-04
 Identities = 14/89 (15%), Positives = 32/89 (35%), Gaps = 7/89 (7%)

Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
           +    + ++YIK    ++T D I+   +  G + +         +        G  FV F
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN------IQMRRTLHKAFKGSIFVVF 54

Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSN 663
            + ES  + ++        E  + +   +
Sbjct: 55  DSIESAKKFVE-TPGQKYKETDLLILFKD 82

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (91), Expect = 7e-05
 Identities = 20/71 (28%), Positives = 24/71 (33%), Gaps = 7/71 (9%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
           I +R L   VT  ++  L   Y              DK KG A VT L  E A  A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 399 DGTVFLGRMLH 409
             +    R L 
Sbjct: 54  HQSRLRERELS 64

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.8 bits (84), Expect = 7e-04
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 9/77 (11%)

Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
           IL+R +P      EV +L   +          K      ++G  FV  +   +A+ A+  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY--------ELKYCFVDKYKGTAFVTLLNGEQAEAAINT 52

Query: 748 LCQSTHLYGRRLVLEWA 764
               + L  R L ++  
Sbjct: 53  -FHQSRLRERELSVQLQ 68

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 8/73 (10%), Positives = 22/73 (30%), Gaps = 5/73 (6%)

Query: 339 IFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
           + + +          L +L E +G ++  ++           F  +       A   Y  
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINE----AFIEMATTEDAQAAVDYYT 66

Query: 398 LDGTVFLGRMLHL 410
               +  G+ + +
Sbjct: 67  TTPALVFGKPVRV 79

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.4 bits (86), Expect = 5e-04
 Identities = 9/88 (10%), Positives = 33/88 (37%), Gaps = 10/88 (11%)

Query: 682 KQTGSK-ILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 739
           +    + + + +       + ++ +L + FG +    +              F+E  T  
Sbjct: 4   RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-------KINEAFIEMATTE 56

Query: 740 EAKRAMKAL-CQSTHLYGRRLVLEWAEE 766
           +A+ A+         ++G+ + +  +++
Sbjct: 57  DAQAAVDYYTTTPALVFGKPVRVHLSQK 84

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 0.001
 Identities = 10/82 (12%), Positives = 23/82 (28%), Gaps = 7/82 (8%)

Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP-EHATQAYQH 397
            F  +L      +DL  LF  +G +  +         +     ++ F    + A    + 
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWID------FVRGAKEGIILFKEKAKEALGKAKD 67

Query: 398 LDGTVFLGRMLHLIPGKPKENE 419
            +      R   +     +   
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEV 89

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 0.002
 Identities = 18/89 (20%), Positives = 29/89 (32%), Gaps = 8/89 (8%)

Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
            D A S  + +R L   VTE ++  L   +G         +    K K  A +     E 
Sbjct: 3   MDGAPSRVLHIRKLPGEVTETEVIALGLPFGK------VTNILMLKGKNQAFLELATEEA 56

Query: 391 ATQA--YQHLDGTVFLGRMLHLIPGKPKE 417
           A     Y          + +++     KE
Sbjct: 57  AITMVNYYSAVTPHLRNQPIYIQYSNHKE 85

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 34.8 bits (79), Expect = 0.004
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
             + + N+P +  +  +  LF  F   K VRL              FVEF T+ ++  A 
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN------RHDIAFVEFTTELQSNAAK 62

Query: 746 KALCQSTHLYGRRLVLEWAEE 766
           +AL          + + +A++
Sbjct: 63  EALQGFKITPTHAMKITFAKK 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	787
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.95
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.93
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.76
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.75
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.75
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.75
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.74
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.74
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.74
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.74
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.73
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.73
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.73
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.73
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.73
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.72
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.72
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.72
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.72
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.72
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.71
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.71
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.71
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.71
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.71
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.7
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.7
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.69
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.69
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.69
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.69
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.68
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.68
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.68
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.68
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.68
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.67
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.67
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.67
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.66
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.66
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.66
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.65
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.65
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.65
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.65
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.65
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.64
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.64
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.64
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.64
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.64
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.64
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.64
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.63
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.63
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.62
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.61
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.61
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.61
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.61
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.61
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.6
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.6
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.6
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.6
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.59
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.59
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.59
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.59
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.59
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.59
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.59
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.59
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.59
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.59
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.59
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.59
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.58
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.57
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.57
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.57
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.57
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.57
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.56
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.56
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.56
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.56
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.55
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.55
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.55
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.54
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.54
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.54
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.54
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.53
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.51
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.49
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.48
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.46
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.44
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.41
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.37
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.35
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.35
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.34
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.31
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.3
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.28
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.27
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.26
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.25
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.2
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.54
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.47
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.32
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.99
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.83
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.29
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	92.99
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	92.92

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=8.3e-28  Score=231.23  Aligned_cols=174  Identities=25%  Similarity=0.439  Sum_probs=151.1

Q ss_pred             CCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Q psy3345         580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIEL  659 (787)
Q Consensus       580 ~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v  659 (787)
                      .++|||+|||+++|+++|+++|++||.|.++.++++..     ++.++|||||+|.+.++|..|+. +++..+.++.+.+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~-----~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~   79 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-----TKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEP   79 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeeccc-----CCCccCceecccCCHHHHHHHHH-hcCCcccccchhh
Confidence            47999999999999999999999999999999998765     67899999999999999999998 5677788888888


Q ss_pred             EecCccccchhhhhhhccccccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHH
Q psy3345         660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN  739 (787)
Q Consensus       660 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~  739 (787)
                      .........        .........++|||+|||..+|+++|+++|+.||.|..+.|+.+. .+|.++|||||.|.+++
T Consensus        80 ~~~~~~~~~--------~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~-~~~~~~g~~fV~f~~~e  150 (183)
T d1u1qa_          80 KRAVSREDS--------QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHD  150 (183)
T ss_dssp             EECCCTTGG--------GSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESCHH
T ss_pred             hhhhhcccc--------cccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccc-ccCccceeEEEEECCHH
Confidence            776543331        111234466899999999999999999999999999999999885 67999999999999999


Q ss_pred             HHHHHHHHhcCCeeecCceEEEEEccccccH
Q psy3345         740 EAKRAMKALCQSTHLYGRRLVLEWAEEADNV  770 (787)
Q Consensus       740 ~A~~Al~~l~~~~~~~Gr~l~v~~A~~~~~~  770 (787)
                      +|.+|+. ++ +..+.|++|.|.||.+++++
T Consensus       151 ~A~~Al~-~~-~~~~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         151 SVDKIVI-QK-YHTVNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             HHHHHHT-SS-CEEETTEEEEEEECCCHHHH
T ss_pred             HHHHHHH-hC-CCeECCEEEEEEecCCcccc
Confidence            9999997 55 58899999999999987543

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=3.8e-25  Score=212.42  Aligned_cols=164  Identities=17%  Similarity=0.258  Sum_probs=140.6

Q ss_pred             ccceEEEeCCCCCCCHHhHHHhhcCCCCc-ceeec-------ccceEEEeecChHhHHHHHhcCCcccCCeeEEEeeccc
Q psy3345         223 QYHTIVVKNLPAGVKKKDLKAYFKPLPLA-SVRTT-------FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSK  294 (787)
Q Consensus       223 ~~~~v~v~nLp~~~te~di~~~F~~~g~v-~i~i~-------~~g~afV~F~~~~~A~~Al~~~~~~l~g~~i~v~~~~~  294 (787)
                      ..++|||+|||+++|+++|+++|+.+|.+ ++.++       ++|+|||+|.+.++|.+|+..++..+.++.+.+.+..+
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            45899999999999999999999999988 67665       56899999999999999999888888888888753211


Q ss_pred             CCccccCCCcCCCCchhhhhhhhcccccccchhhhhcccCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCC
Q psy3345         295 DNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET  374 (787)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  374 (787)
                      ....                             .........++|||+|||+.+|+++|+++|+.||.|..+.++.+..+
T Consensus        85 ~~~~-----------------------------~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~  135 (183)
T d1u1qa_          85 REDS-----------------------------QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS  135 (183)
T ss_dssp             TTGG-----------------------------GSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTT
T ss_pred             cccc-----------------------------cccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccccc
Confidence            1110                             01122345678999999999999999999999999999999999888


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         375 DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       375 ~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      |.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++.++
T Consensus       136 ~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         136 GKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             CccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            9999999999999999999997 7999999999999998765

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=8.2e-20  Score=152.58  Aligned_cols=89  Identities=74%  Similarity=1.191  Sum_probs=81.7

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||+.+|+++|+++|+.||.|.+|+|+++...+|+++|||||+|.++++|.+|++.|+|+..++|++|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            34678899999999999999999999999999999998865689999999999999999999999995579999999999


Q ss_pred             EEccccccH
Q psy3345         762 EWAEEADNV  770 (787)
Q Consensus       762 ~~A~~~~~~  770 (787)
                      +||+++...
T Consensus        85 ~~A~~~~~~   93 (94)
T d2cpha1          85 EWADSEVTV   93 (94)
T ss_dssp             EECCCCCCC
T ss_pred             EEcCCCCCc
Confidence            999987653

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.78  E-value=3.2e-19  Score=145.37  Aligned_cols=80  Identities=25%  Similarity=0.544  Sum_probs=76.3

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      +++|||+|||+++|+++|+++|++||.|.+++|+++. .+|+++|||||+|.++++|.+|++.|| +..+.|++|+|+||
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~~g~~~g~afV~f~~~~~A~~ai~~ln-g~~~~g~~l~v~~a   79 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY-KTGYSYGYAFVDFTSEMDSQRAIKVLN-GITVRNKRLKVSYA   79 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET-TTTEECSEEEEEESSHHHHHHHHHHHT-TCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec-ccCCccccceEEECCHHHHHHHHHHhC-CCEECCEEEEEEEc
Confidence            5789999999999999999999999999999999875 689999999999999999999999997 79999999999999


Q ss_pred             cc
Q psy3345         765 EE  766 (787)
Q Consensus       765 ~~  766 (787)
                      +|
T Consensus        80 ~p   81 (82)
T d1b7fa1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             CC
Confidence            87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.77  E-value=5.9e-19  Score=145.42  Aligned_cols=84  Identities=26%  Similarity=0.495  Sum_probs=77.9

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ...+++|||+|||..+|+++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..|| +..+.|++|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~-~tg~~~g~afV~f~~~~~A~~A~~~ln-g~~l~g~~l~V   81 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAAKEALN-GAEIMGQTIQV   81 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTSSEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccc-cccccccceeEEECCHHHHHHHHHHcC-CCEECCEEEEE
Confidence            3457899999999999999999999999999999999885 689999999999999999999999997 69999999999


Q ss_pred             EEcccc
Q psy3345         762 EWAEEA  767 (787)
Q Consensus       762 ~~A~~~  767 (787)
                      +||.++
T Consensus        82 ~~a~~k   87 (88)
T d1rk8a_          82 DWCFVK   87 (88)
T ss_dssp             EESEEC
T ss_pred             EEecCC
Confidence            999865

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=7.5e-19  Score=143.18  Aligned_cols=80  Identities=25%  Similarity=0.514  Sum_probs=75.9

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      .++|||+|||..+|+++|+++|++||.|.+++|+++. .+|.++|||||+|.++++|..|++.|| +..+.|++|+|+||
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~-g~~~~g~~l~v~~A   79 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK-ITGQSLGYGFVNYIDPKDAEKAINTLN-GLRLQTKTIKVSYA   79 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHHT-TCEETTEECEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeec-cCCCceeeEEEEECCHHHHHHHHHHhC-CCEECCEEEEEEEe
Confidence            4689999999999999999999999999999999875 678999999999999999999999997 79999999999999


Q ss_pred             cc
Q psy3345         765 EE  766 (787)
Q Consensus       765 ~~  766 (787)
                      +|
T Consensus        80 kP   81 (82)
T d1fxla1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             eC
Confidence            87

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=5e-19  Score=146.66  Aligned_cols=85  Identities=27%  Similarity=0.540  Sum_probs=79.5

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||..+|+++|+++|++||.|.+++|+++. .+|.++|||||+|.+.++|.+|++.|| +..+.|++|+|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~-~t~~~rg~afV~f~~~~~A~~Ai~~l~-g~~~~g~~i~v~   83 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK-TTGQSKGFAFISFHRREDAARAIAGVS-GFGYDHLILNVE   83 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHHHHHTT-TCEETTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccc-cccccccceeEEECCHHHHHHHHHHhC-CCEECCEEEEEE
Confidence            456789999999999999999999999999999999985 589999999999999999999999997 799999999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||+|..+
T Consensus        84 ~akp~~n   90 (90)
T d2cq0a1          84 WAKPSTN   90 (90)
T ss_dssp             ESSCCCC
T ss_pred             eeeCCCC
Confidence            9998764

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=9.6e-19  Score=147.88  Aligned_cols=84  Identities=14%  Similarity=0.230  Sum_probs=79.0

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      +....+.+|+|.|     ||+++|++||+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|++||+.||+..|+|
T Consensus         3 ~~~~~~~~lfV~n-----L~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (99)
T d1whwa_           3 SGSSGSGRLFVRN-----LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG   77 (99)
T ss_dssp             CCCCSCEEEEEEC-----CCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS
T ss_pred             CCCCCCCEEEEEC-----CCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECC
Confidence            3445577899999     99999999999999999999999999987 79999999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      |.|+|.+|.+
T Consensus        78 r~i~V~~a~~   87 (99)
T d1whwa_          78 RMLHVLPSTI   87 (99)
T ss_dssp             CEEEEEECCC
T ss_pred             EEEEEEECCC
Confidence            9999999987

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1e-18  Score=148.22  Aligned_cols=86  Identities=16%  Similarity=0.371  Sum_probs=80.3

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..++++|||+|||+.+|+++|+++|+.||.|.+++++.+. .+|+++|||||+|.++++|..||+.|| +..+.|++|+|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~-~~g~~kG~afV~f~~~~~A~~Ai~~ln-g~~~~g~~i~V   92 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK-QTNLSKCFGFVSYDNPVSAQAAIQSMN-GFQIGMKRLKV   92 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECS-SSCSEEEEEEEECSSHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeec-ccCCCccceEEEeCCHHHHHHHHHHhC-CCEECCEEEEE
Confidence            3467889999999999999999999999999999998875 689999999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      +||.++++
T Consensus        93 ~~a~~k~~  100 (102)
T d2cpza1          93 QLKRSKND  100 (102)
T ss_dssp             ECCCCSCC
T ss_pred             EEeCCCCC
Confidence            99998875

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=8.5e-19  Score=141.65  Aligned_cols=79  Identities=18%  Similarity=0.375  Sum_probs=74.8

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccc
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE  766 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~  766 (787)
                      .|||+|||+.+|+++|+++|++||.|.+++|+++. .+|+++|||||+|.++++|..|++.|+ |..+.||+|+|+||+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~~~g~aFV~f~~~~~a~~ai~~l~-g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM-ITRRSLGYAYVNFQQPADAERALDTMN-FDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHTTST-TCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecc-cccCCCCceEEEECCHHHHHHHHHHcC-CCEECCEEEEEEEeCC
Confidence            69999999999999999999999999999999986 679999999999999999999999997 7999999999999975


Q ss_pred             c
Q psy3345         767 A  767 (787)
Q Consensus       767 ~  767 (787)
                      +
T Consensus        80 d   80 (80)
T d1cvja1          80 D   80 (80)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.5e-18  Score=144.51  Aligned_cols=84  Identities=26%  Similarity=0.480  Sum_probs=78.9

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||..+|+++|+++|++||.|.+++|+++. .+|.++|||||+|.+.++|..|++.|| +..+.|+.|+|+
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~-~tg~~kg~afV~f~~~~~A~~Ai~~l~-g~~~~g~~l~V~   84 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-VTGQHQGYGFVEFLSEEDADYAIKIMD-MIKLYGKPIRVN   84 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCSBCSCEEEEESSHHHHHHHHHHSS-SCBCSSCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecc-cccccccceEEEECCHHHHHHHHHHcC-CCEECCEEEEEE
Confidence            456899999999999999999999999999999999885 689999999999999999999999997 799999999999


Q ss_pred             Eccccc
Q psy3345         763 WAEEAD  768 (787)
Q Consensus       763 ~A~~~~  768 (787)
                      ||.+++
T Consensus        85 ~A~~~~   90 (93)
T d1x5ua1          85 KASAHN   90 (93)
T ss_dssp             ETTTTS
T ss_pred             EcCCCC
Confidence            999765

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=8.3e-19  Score=140.86  Aligned_cols=76  Identities=14%  Similarity=0.310  Sum_probs=73.7

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEc
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      ||+|.|     ||+++|++||+++|+.||.|.+|+|+.+++|+++|||||.|.++++|++|++.||+..++||.|.|.+|
T Consensus         2 rl~V~n-----Lp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSN-----LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV   76 (78)
T ss_dssp             EEEEES-----CCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             EEEEEC-----CCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            688888     999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             c
Q psy3345          94 S   94 (787)
Q Consensus        94 ~   94 (787)
                      .
T Consensus        77 ~   77 (78)
T d1no8a_          77 T   77 (78)
T ss_dssp             C
T ss_pred             e
Confidence            5

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.75  E-value=1.5e-18  Score=142.85  Aligned_cols=83  Identities=19%  Similarity=0.334  Sum_probs=77.4

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ++....|+|.|     ||+++|++||+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|++|++.||+..|+||.
T Consensus         4 s~~~~~l~V~n-----L~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~   78 (88)
T d1rk8a_           4 SVEGWILFVTS-----IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT   78 (88)
T ss_dssp             CC-CEEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEE
Confidence            44567799999     99999999999999999999999999987 7999999999999999999999999999999999


Q ss_pred             EEEEEccCC
Q psy3345          88 IKVEKCSNL   96 (787)
Q Consensus        88 i~v~~~~~~   96 (787)
                      |.|++|.+.
T Consensus        79 l~V~~a~~k   87 (88)
T d1rk8a_          79 IQVDWCFVK   87 (88)
T ss_dssp             CEEEESEEC
T ss_pred             EEEEEecCC
Confidence            999999873

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=9e-19  Score=144.73  Aligned_cols=84  Identities=24%  Similarity=0.455  Sum_probs=78.5

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||..+|+++|+++|++||.|.+|+|+++. .+|+++|||||+|.+.++|.+|+..|| +..+.|++|.|+|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~~~~~kg~afV~f~~~~~A~~ai~~l~-~~~i~g~~l~v~~   81 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMN-ESELFGRTIRVNL   81 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCS-SSCCCSSEEEECCSSHHHHHHHHHHHT-TEEETTEEEEEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEeccccccc-ccccccceeEEEECCHHHHHHHHHHcC-CCEECCEEEEEEE
Confidence            45789999999999999999999999999999999986 689999999999999999999999997 7999999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      |+|+..
T Consensus        82 a~p~~~   87 (89)
T d2cqba1          82 AKPMRI   87 (89)
T ss_dssp             CCCCCC
T ss_pred             eCCCCC
Confidence            998653

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.7e-18  Score=142.86  Aligned_cols=84  Identities=24%  Similarity=0.427  Sum_probs=78.2

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ..+++|||+|||..+|+++|+++|++||.|.+|+|+++. .+|.++|||||+|.+.++|..|++.|| +..++|++|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~~~~kg~afV~f~~~~~A~~Ai~~l~-g~~~~gr~i~V~   82 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKKTACGFCFVEYYSRADAENAMRYIN-GTRLDDRIIRTD   82 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHTT-TSEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceecccccc-ccccccceEEEEECCHHHHHHHHHHhC-CCEECCEEEEEE
Confidence            467899999999999999999999999999999999886 689999999999999999999999997 799999999999


Q ss_pred             Eccccc
Q psy3345         763 WAEEAD  768 (787)
Q Consensus       763 ~A~~~~  768 (787)
                      ||....
T Consensus        83 ~a~~~~   88 (93)
T d1h2vz_          83 WDAGFK   88 (93)
T ss_dssp             EESCCC
T ss_pred             EcCCCC
Confidence            997543

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.75  E-value=1.3e-18  Score=141.63  Aligned_cols=79  Identities=20%  Similarity=0.293  Sum_probs=75.4

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      .+.|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.++++|++||+.||+..++|+.|.|
T Consensus         2 ~t~l~V~n-----Lp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v   76 (82)
T d1b7fa1           2 NTNLIVNY-----LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKV   76 (82)
T ss_dssp             CSEEEEEC-----CCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEeC-----CCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            45689999     99999999999999999999999999987 7999999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|+|
T Consensus        77 ~~a~p   81 (82)
T d1b7fa1          77 SYARP   81 (82)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99986

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.8e-18  Score=139.76  Aligned_cols=79  Identities=19%  Similarity=0.332  Sum_probs=75.5

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      +++|+|.|     ||+++|++||+++|+.||.|.+|+|+.+. .|+++|||||.|.++++|++|++.|||..|+|+.|.|
T Consensus         2 ~t~l~V~n-----Lp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v   76 (82)
T d1fxla1           2 KTNLIVNY-----LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV   76 (82)
T ss_dssp             CSEEEEES-----CCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEEC-----CCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            46789999     99999999999999999999999999977 7899999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|+|
T Consensus        77 ~~AkP   81 (82)
T d1fxla1          77 SYARP   81 (82)
T ss_dssp             EECCC
T ss_pred             EEeeC
Confidence            99986

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.6e-18  Score=142.21  Aligned_cols=83  Identities=19%  Similarity=0.265  Sum_probs=78.5

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      ...++..|+|.|     ||+++|+++|+++|+.||.|..|+|+.++ +|+++|||||.|.+.++|.+||+.||+..|+|+
T Consensus         4 ~~~~~~~i~V~n-----Lp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~   78 (90)
T d2cq0a1           4 RADDNATIRVTN-----LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL   78 (90)
T ss_dssp             CCSSSEEEEEES-----CCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCCCEEEEEC-----CCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCE
Confidence            445677899999     99999999999999999999999999987 699999999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|+|
T Consensus        79 ~i~v~~akp   87 (90)
T d2cq0a1          79 ILNVEWAKP   87 (90)
T ss_dssp             ECEEEESSC
T ss_pred             EEEEEeeeC
Confidence            999999987

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=3.4e-18  Score=137.21  Aligned_cols=76  Identities=33%  Similarity=0.476  Sum_probs=72.9

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      +|||+|||+.+|+++|+++|++||.|.+++|+.+  .+|+++|||||+|.++++|.+|++.|| +..+.|++|+|+||.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~--~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD--RSGRSLGTADVHFERKADALKAMKQYN-GVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCS--SCCCSCCEEEEEESCHHHHHHHHHHHT-TCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe--eccccceeEEEEECCHHHHHHHHHHhC-CCEECCEEEEEEEee
Confidence            5999999999999999999999999999999998  489999999999999999999999997 799999999999985

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.1e-18  Score=140.31  Aligned_cols=80  Identities=19%  Similarity=0.262  Sum_probs=74.1

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +-.+++|+|.|     ||+++|+++|+++|+.||.|.+|+|++++ +|+++|||||.|.++++|.+||+.+  ..|+||.
T Consensus         5 ~~~~~~lfV~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~   77 (90)
T d2cqga1           5 VQKTSDLIVLG-----LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRW   77 (90)
T ss_dssp             CCCCCCEEEES-----CCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEE
T ss_pred             CcCCCeEEEEC-----CCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEE
Confidence            34567899999     99999999999999999999999999988 6999999999999999999999864  4899999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|.+
T Consensus        78 i~v~~a~~   85 (90)
T d2cqga1          78 CDCKLPNS   85 (90)
T ss_dssp             EEEECCCT
T ss_pred             eEEEeCCC
Confidence            99999986

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2e-18  Score=141.00  Aligned_cols=78  Identities=15%  Similarity=0.227  Sum_probs=75.1

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      .+|+|.|     ||+++|++||+++|+.||+|.+|+|++++ +|+++|||||.|.++++|..|++.||+..|+|+.|.|.
T Consensus         2 ~rlfV~n-----lp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~   76 (85)
T d2u2fa_           2 HKLFIGG-----LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ   76 (85)
T ss_dssp             CCEEEET-----CCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEE
T ss_pred             CEEEEEC-----CCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4789999     99999999999999999999999999988 69999999999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +|.+
T Consensus        77 ~A~~   80 (85)
T d2u2fa_          77 RASV   80 (85)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9986

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.8e-18  Score=144.05  Aligned_cols=81  Identities=19%  Similarity=0.231  Sum_probs=77.1

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ++.+|+|.|     ||+++|++||+++|+.||.|.+|.+++++ +|+++|||||.|.++++|..||+.||+..|+|+.|.
T Consensus        17 ~~~~l~V~n-----Lp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~   91 (102)
T d2cpza1          17 EGANLFIYH-----LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   91 (102)
T ss_dssp             TTCCEEEES-----CCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            567899999     99999999999999999999999999987 799999999999999999999999999999999999


Q ss_pred             EEEccCC
Q psy3345          90 VEKCSNL   96 (787)
Q Consensus        90 v~~~~~~   96 (787)
                      |.+|++.
T Consensus        92 V~~a~~k   98 (102)
T d2cpza1          92 VQLKRSK   98 (102)
T ss_dssp             EECCCCS
T ss_pred             EEEeCCC
Confidence            9999873

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=7.4e-18  Score=142.33  Aligned_cols=85  Identities=24%  Similarity=0.421  Sum_probs=79.2

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||+.+|+++|+++|++||.|.+++|+++. .+|+++|||||+|.+.++|..||+.|| +..+.|++|+|+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~-~tg~~~g~afV~f~~~~~a~~A~~~l~-g~~~~gr~i~V~   83 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS-LTKKPKGFAFVTFMFPEHAVKAYAEVD-GQVFQGRMLHVL   83 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT-TTCCCCSEEEEEESSHHHHHHHHHHTT-TEESSSCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccc-cccccCcceEEEECCHHHHHHHHHHcC-CCEECCEEEEEE
Confidence            356789999999999999999999999999999999885 689999999999999999999999997 699999999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||.++..
T Consensus        84 ~a~~~~~   90 (99)
T d1whwa_          84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             ECCCCCc
Confidence            9997654

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=3.8e-18  Score=138.43  Aligned_cols=80  Identities=15%  Similarity=0.284  Sum_probs=69.2

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      .++|||+|||+.+|+++|+++|++||.|..+.++.+. ..|+++|||||+|.++++|.+|++.|| +..+.|++|+|+||
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~~g~afV~f~~~e~A~~Ai~~l~-g~~~~g~~i~V~~a   78 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL-RFNTSRRFAYIDVTSKEDARYCVEKLN-GLKIEGYTLVTKVS   78 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHT-TCEETTEECEEEEC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeeccc-ccccccceeEEEECCHHHHHHHHHHhC-CCEECCEEEEEEEc
Confidence            3789999999999999999999999999888776664 689999999999999999999999997 79999999999999


Q ss_pred             cc
Q psy3345         765 EE  766 (787)
Q Consensus       765 ~~  766 (787)
                      +|
T Consensus        79 ~P   80 (81)
T d2ghpa1          79 NP   80 (81)
T ss_dssp             CC
T ss_pred             cC
Confidence            98

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=5.7e-18  Score=138.39  Aligned_cols=79  Identities=28%  Similarity=0.519  Sum_probs=73.6

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC--ceEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG--RRLVL  761 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G--r~l~v  761 (787)
                      .+++|||+|||..+|+++|+++|++||.|.+++|+++. .+|+++|||||+|.++++|.+|++.|| +..+.|  ++|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~g~~kg~afV~f~~~~~a~~Ai~~ln-g~~~~G~~~~i~V   82 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ-VTGVSRGVGFIRFDKRIEAEEAIKGLN-GQKPSGATEPITV   82 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHHT-TCCCTTCSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccccc-ccccCCCeeEEEEcCHHHHHHHHHHhC-CCEeCCCCEEEEE
Confidence            35789999999999999999999999999999999885 679999999999999999999999997 699988  56999


Q ss_pred             EEc
Q psy3345         762 EWA  764 (787)
Q Consensus       762 ~~A  764 (787)
                      .||
T Consensus        83 ~~A   85 (85)
T d1fxla2          83 KFA   85 (85)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            998

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.9e-18  Score=138.29  Aligned_cols=83  Identities=25%  Similarity=0.530  Sum_probs=76.4

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||+.+|+++|+++|++||.|.+|+|+++. .+|+++|||||.|.++++|.+||+.   ...++||.|.|.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~srG~aFV~f~~~~~a~~al~~---~~~l~Gr~i~v~   81 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL-KTGHSKGFGFVRFTEYETQVKVMSQ---RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHHHHS---CEEETTEEEEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCC-CCcccCCEEEEEECCHHHHHHHHhc---CCccCCEEeEEE
Confidence            456889999999999999999999999999999999986 6899999999999999999999984   358999999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||.+++.
T Consensus        82 ~a~~k~~   88 (90)
T d2cqga1          82 LPNSKQS   88 (90)
T ss_dssp             CCCTTCC
T ss_pred             eCCCCCC
Confidence            9998764

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8e-18  Score=137.10  Aligned_cols=77  Identities=25%  Similarity=0.403  Sum_probs=72.9

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      +.|+..|+|.|     ||+.+|+++|+++|+.||.|.+|+|++++ +|+++|||||.|.+.++|.+|++.||+..|+||.
T Consensus         6 p~~~~~l~V~n-----L~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~   80 (83)
T d2cqca1           6 PDPNCCLGVFG-----LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR   80 (83)
T ss_dssp             CCGGGCEEEES-----CCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            34677899999     99999999999999999999999999987 6999999999999999999999999999999999


Q ss_pred             EEE
Q psy3345          88 IKV   90 (787)
Q Consensus        88 i~v   90 (787)
                      |+|
T Consensus        81 i~V   83 (83)
T d2cqca1          81 IRV   83 (83)
T ss_dssp             EEE
T ss_pred             eEC
Confidence            987

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=4e-18  Score=145.51  Aligned_cols=89  Identities=27%  Similarity=0.518  Sum_probs=81.5

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      .++|||+|||..+|+++|+++|++||.|.+|+|+++. .+|+++|||||+|.+.++|..|++.|| +..+.|++|+|+||
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~-~tg~~~g~afV~f~~~~~a~~ai~~l~-~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQETALSAMRNLN-GREFSGRALRVDNA   85 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET-TTTEEEEEEEEECSCHHHHHHHHHHSS-SBSCSSSCBEEEET
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhcccccccccccccc-ceeccCCceEEEECCHHHHHHHHHHcC-CCEECCEEEEEEEC
Confidence            3579999999999999999999999999999999885 679999999999999999999999997 79999999999999


Q ss_pred             cccccHHHHHH
Q psy3345         765 EEADNVEDIRK  775 (787)
Q Consensus       765 ~~~~~~~~~~~  775 (787)
                      .++...++.+.
T Consensus        86 ~~~~~~~~~~~   96 (104)
T d1p1ta_          86 ASEKNKEELKS   96 (104)
T ss_dssp             TCTTHHHHHHH
T ss_pred             CCCCCcccccc
Confidence            98877655554

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.73  E-value=7.5e-18  Score=137.88  Aligned_cols=79  Identities=23%  Similarity=0.424  Sum_probs=74.0

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC--ceEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG--RRLVL  761 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G--r~l~v  761 (787)
                      ..++|||.|||..+|+++|+++|++||.|.+++|+++. .+|+++|||||+|.++++|.+|++.|| +..+.|  ++|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~-~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~~~l~V   82 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK-LTGRPRGVAFVRYNKREEAQEAISALN-NVIPEGGSQPLSV   82 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHHT-TCCCTTCSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeeccc-ccccCceeEEEEECCHHHHHHHHHHHC-CCEeCCCCeEEEE
Confidence            56789999999999999999999999999999999885 689999999999999999999999997 688876  89999


Q ss_pred             EEc
Q psy3345         762 EWA  764 (787)
Q Consensus       762 ~~A  764 (787)
                      .||
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            998

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.9e-18  Score=140.09  Aligned_cols=81  Identities=27%  Similarity=0.526  Sum_probs=76.2

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      .+|||+|||..+|+++|+++|++||.|.+++|+++. .+|.++|||||+|.++++|..|+..|| +..+.|++|.|+||.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~-~tg~~rg~aFV~f~~~~~A~~a~~~l~-~~~l~g~~l~V~~A~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQAIAGLN-GMQLGDKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCC-SSSCCCCEEEEEESSSHHHHHHHHTSS-SCCCSSSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccc-cccccceeEEEEECCHHHHHHHHHHhC-CCEECCEEEEEEECC
Confidence            369999999999999999999999999999999985 689999999999999999999999997 799999999999998


Q ss_pred             ccc
Q psy3345         766 EAD  768 (787)
Q Consensus       766 ~~~  768 (787)
                      +..
T Consensus        80 ~~~   82 (85)
T d2u2fa_          80 VGA   82 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.72  E-value=9.2e-18  Score=137.33  Aligned_cols=81  Identities=21%  Similarity=0.366  Sum_probs=75.3

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC-
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS-   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~-   85 (787)
                      ..+..++|+|.|     ||+++||++|+++|+.||.|.+|+|++++ +|+++|||||.|.++++|.+||+.||+..+.| 
T Consensus         2 ~~~~~t~lfV~n-----lp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   76 (85)
T d1b7fa2           2 ESIKDTNLYVTN-----LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG   76 (85)
T ss_dssp             STTTTCEEEEES-----CCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCCCCCEEEEeC-----CCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            345677899999     99999999999999999999999999987 79999999999999999999999999999877 


Q ss_pred             -ceEEEEEc
Q psy3345          86 -SRIKVEKC   93 (787)
Q Consensus        86 -~~i~v~~~   93 (787)
                       |.|.|.+|
T Consensus        77 ~~~l~V~~A   85 (85)
T d1b7fa2          77 SQPLSVRLA   85 (85)
T ss_dssp             SSCCEEEEC
T ss_pred             CeEEEEEEC
Confidence             88999986

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.1e-17  Score=139.14  Aligned_cols=80  Identities=18%  Similarity=0.297  Sum_probs=76.5

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ++..|+|.|     ||+++|+++|+++|+.||.|.+|.|+.++ +|+++|||||.|.+.++|..|++.||+..|+||.|.
T Consensus         6 ~s~tlfV~n-----lp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~   80 (93)
T d1h2vz_           6 KSCTLYVGN-----LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR   80 (93)
T ss_dssp             TCCEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            567899999     99999999999999999999999999988 799999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |++|..
T Consensus        81 V~~a~~   86 (93)
T d1h2vz_          81 TDWDAG   86 (93)
T ss_dssp             EEEESC
T ss_pred             EEEcCC
Confidence            999975

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=8.8e-18  Score=135.59  Aligned_cols=77  Identities=26%  Similarity=0.406  Sum_probs=75.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      +|||+|||+.+|+++|+++|++||+|.+|+|++++.+|+++|||||+|.++++|..|++.|+|..+.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999986

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.9e-17  Score=137.78  Aligned_cols=83  Identities=30%  Similarity=0.490  Sum_probs=76.4

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||+|||+.+|+++|+++|++||.|.+|+++.+.   +.++|||||+|.++++|.+|+..|| +..+.|++|+|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~---~~~kg~afV~f~~~~~a~~Ai~~l~-~~~~~g~~l~V   83 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE---RGSKGFGFVTFENSADADRAREKLH-GTVVEGRKIEV   83 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT---TTTCCEEEEEESCHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc---cCCcceeEEEECCHHHHHHHHHHcC-CCEECCEEEEE
Confidence            4467889999999999999999999999999999999883   4579999999999999999999997 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      +||+++.
T Consensus        84 ~~A~~r~   90 (93)
T d2cq3a1          84 NNATARV   90 (93)
T ss_dssp             EECCSSC
T ss_pred             EecCcCC
Confidence            9999764

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=6.6e-18  Score=140.83  Aligned_cols=81  Identities=19%  Similarity=0.398  Sum_probs=76.1

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC--CCCcceEEEEEecCHHHHHHHHHHh-ccCccCCc
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT--EGKFRRFAFIGYHREDQAQAALDYF-NNTYVFSS   86 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~~~-~~~~~~~~   86 (787)
                      -++++|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++  +|+++|||||.|.++++|.+||+.| |+..|+||
T Consensus         6 ~~~~~l~V~n-----Lp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr   80 (94)
T d2cpha1           6 QTTSKILVRN-----IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   80 (94)
T ss_dssp             SCCCCEEEES-----CCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCE
Confidence            3567899999     99999999999999999999999999875  6999999999999999999999998 88999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      +|.|.+|++
T Consensus        81 ~l~V~~A~~   89 (94)
T d2cpha1          81 RLVLEWADS   89 (94)
T ss_dssp             BCEEEECCC
T ss_pred             EEEEEEcCC
Confidence            999999986

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.72  E-value=6.9e-18  Score=138.24  Aligned_cols=82  Identities=22%  Similarity=0.445  Sum_probs=71.4

Q ss_pred             CCCEEEEecCCccCc-HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         684 TGSKILVRNIPFQAK-QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t-~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+++|||+|||+++| +++|+++|++||.|.+|+|+.+...+|+++|||||+|.+.++|.+|++ || +..+.|+.|.|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n-~~~~~gr~l~V~   80 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MN-RSLLGNREISVS   80 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GT-TEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cC-CCEECCEEEEEE
Confidence            467999999999986 556999999999999999987644689999999999999999999996 86 799999999999


Q ss_pred             Ecccc
Q psy3345         763 WAEEA  767 (787)
Q Consensus       763 ~A~~~  767 (787)
                      ||+++
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99864

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=2.5e-18  Score=137.15  Aligned_cols=74  Identities=18%  Similarity=0.253  Sum_probs=70.2

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      +|+|.|     ||+++|+++|+++|+.||.|.+|+|++++ +|+++|||||+|.++++|++||+ +|++.|+||.|+|..
T Consensus         2 klfV~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~   75 (77)
T d1uawa_           2 KMFIGG-----LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKV   75 (77)
T ss_dssp             CEEEES-----CCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEE
T ss_pred             EEEEeC-----CCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEE
Confidence            578888     99999999999999999999999999988 69999999999999999999998 599999999999987


Q ss_pred             c
Q psy3345          93 C   93 (787)
Q Consensus        93 ~   93 (787)
                      |
T Consensus        76 A   76 (77)
T d1uawa_          76 A   76 (77)
T ss_dssp             C
T ss_pred             C
Confidence            7

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=4.5e-18  Score=140.48  Aligned_cols=80  Identities=25%  Similarity=0.418  Sum_probs=75.9

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .+..|+|.|     ||+++|+++|+++|+.||.|.+|.|++++ +|+++|||||.|.+.++|.+|++.||+..|+|+.|.
T Consensus         4 ~~~tlfV~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~   78 (89)
T d2cqba1           4 TKRVLYVGG-----LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   78 (89)
T ss_dssp             CCSCEEEES-----CCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCcEEEEeC-----CCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            345689999     99999999999999999999999999988 699999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|+|
T Consensus        79 v~~a~p   84 (89)
T d2cqba1          79 VNLAKP   84 (89)
T ss_dssp             EEECCC
T ss_pred             EEEeCC
Confidence            999986

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.1e-17  Score=138.76  Aligned_cols=84  Identities=27%  Similarity=0.524  Sum_probs=77.5

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ...+|||+|||+.+|+++|+++|++||.|..+.++.+. .+|.++|||||.|.++++|..|++.|+ +..++|++|+|+|
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~-~~~~~~g~afV~f~~~~~a~~Ai~~l~-~~~~~g~~l~V~~   81 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-ETQRSRGFGFVTFENIDDAKDAMMAMN-GKSVDGRQIRVDQ   81 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS-SSCSCCSEEEEECSSHHHHHHHHHHHT-TCCTTSCCCEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeecccc-ccccccceEEEEECCHHHHHHHHHHcC-CCEECCEEEEEEE
Confidence            35679999999999999999999999999999988775 689999999999999999999999997 6999999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      |.++.+
T Consensus        82 a~~~~~   87 (90)
T d1x5sa1          82 AGKSSD   87 (90)
T ss_dssp             EECCCC
T ss_pred             cCCCCC
Confidence            987653

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.6e-17  Score=136.92  Aligned_cols=82  Identities=17%  Similarity=0.396  Sum_probs=75.9

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ......+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++.+ ++|||||.|.++++|.+|++.||+..|+||+
T Consensus         7 ~~~~~~~l~v~n-----Lp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~   80 (93)
T d2cq3a1           7 SKSTPKRLHVSN-----IPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRK   80 (93)
T ss_dssp             CSCCCCEEEEES-----CCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEEC-----CCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            344566799999     9999999999999999999999999998654 7999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|++
T Consensus        81 l~V~~A~~   88 (93)
T d2cq3a1          81 IEVNNATA   88 (93)
T ss_dssp             CEEEECCS
T ss_pred             EEEEecCc
Confidence            99999997

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.4e-17  Score=141.42  Aligned_cols=81  Identities=19%  Similarity=0.193  Sum_probs=74.8

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ...+|+|.|     ||+++||+||+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+||+.+|+ .|+||.|.
T Consensus         9 ~~~~lfV~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~   82 (103)
T d2cqda1           9 TFTKIFVGG-----LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   82 (103)
T ss_dssp             SSSEEEEEC-----CCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CCcEEEEeC-----CCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEE
Confidence            346799999     99999999999999999999999999988 699999999999999999999999765 79999999


Q ss_pred             EEEccCCC
Q psy3345          90 VEKCSNLG   97 (787)
Q Consensus        90 v~~~~~~~   97 (787)
                      |.+|....
T Consensus        83 V~~a~~~~   90 (103)
T d2cqda1          83 VNLAYLGA   90 (103)
T ss_dssp             EEESTTTC
T ss_pred             EEEcCCCC
Confidence            99998643

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=6.8e-18  Score=137.58  Aligned_cols=80  Identities=20%  Similarity=0.426  Sum_probs=73.9

Q ss_pred             EEEecCCccCcHHHHHHHHHhcCCeeEE-EeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccc
Q psy3345         688 ILVRNIPFQAKQSEVEELFKAFGELKFV-RLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE  766 (787)
Q Consensus       688 l~V~nLp~~~t~~dL~~~F~~~G~I~~v-~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~  766 (787)
                      |||+|||+.+|+++|+++|++||.|.++ +|+++. .+|+++|||||+|.++++|.+|++.|+ +..+.|++|+|+||.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~Ai~~~~-g~~~~gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP-DTGNSKGYAFINFASFDASDAAIEAMN-GQYLCNRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT-TTCSCCSEEEEEBSSHHHHHHHHHTTT-TCEETTEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeec-cccccCceEEEEECCHHHHHHHHHhCC-CcEECCEEEEEEEecC
Confidence            7999999999999999999999999664 788875 689999999999999999999999997 7999999999999998


Q ss_pred             ccc
Q psy3345         767 ADN  769 (787)
Q Consensus       767 ~~~  769 (787)
                      ++.
T Consensus        79 k~~   81 (83)
T d1x5ta1          79 KDS   81 (83)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            764

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.5e-17  Score=138.40  Aligned_cols=82  Identities=26%  Similarity=0.442  Sum_probs=78.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      ..++|||+|||+++|+++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy3345         415 PK  416 (787)
Q Consensus       415 ~~  416 (787)
                      ++
T Consensus        88 ~~   89 (93)
T d1x5ua1          88 AH   89 (93)
T ss_dssp             TT
T ss_pred             CC
Confidence            65

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=5.8e-18  Score=134.58  Aligned_cols=74  Identities=20%  Similarity=0.373  Sum_probs=69.2

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      +|+|.|     ||+++||++|+++|+.||.|.+|.|+.++ +|+++|||||.|.++++|++||+ +++..|+||.|+|..
T Consensus         1 klfV~n-----l~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGG-----LSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEEC-----CCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeC-----CCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            578888     99999999999999999999999999988 69999999999999999999998 599999999999965


Q ss_pred             c
Q psy3345          93 C   93 (787)
Q Consensus        93 ~   93 (787)
                      |
T Consensus        75 A   75 (75)
T d1hd0a_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=8.8e-18  Score=138.69  Aligned_cols=81  Identities=21%  Similarity=0.400  Sum_probs=75.1

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      ..+|||+|||..+|+++|+++|+.||.|.+++|+.+   .+.++|||||+|.+.++|.+|++.|| |..+.|++|.|+||
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~kg~afV~f~~~~~A~~Ai~~l~-g~~~~g~~i~V~~a   83 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD---ENGSKGYGFVHFETQEAAERAIEKMN-GMLLNDRKVFVGRF   83 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCB---TTBCCSCEEEEESCHHHHHHHTTSSS-EEEETTEEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEee---cCCCcceeEEEECCHHHHHHHHHHcC-CCEECCEEEEEEEC
Confidence            457999999999999999999999999999999988   35589999999999999999999997 79999999999999


Q ss_pred             ccccc
Q psy3345         765 EEADN  769 (787)
Q Consensus       765 ~~~~~  769 (787)
                      +++.+
T Consensus        84 ~~~~~   88 (89)
T d1cvja2          84 KSRKE   88 (89)
T ss_dssp             CCTTT
T ss_pred             CCCCC
Confidence            97754

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=3.3e-17  Score=135.47  Aligned_cols=84  Identities=19%  Similarity=0.376  Sum_probs=75.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||+|||..+|+++|+++|+.||.|.+|+|+++.   ...+|||||+|.+.++|.+|+..|+ +..+.|+.|+|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~~~~~~afV~f~~~~~A~~A~~~l~-~~~~~g~~i~v   80 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH---TSNDPYCFVEFYEHRDAAAALAAMN-GRKILGKEVKV   80 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC---CSSCCEEEEEESSHHHHHHHHHHHT-TEEETTEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeeccc---CccceeeEEEECCHHHHHHHHHHcC-CCEECCEEEEE
Confidence            3456799999999999999999999999999999999883   3358999999999999999999997 79999999999


Q ss_pred             EEcccccc
Q psy3345         762 EWAEEADN  769 (787)
Q Consensus       762 ~~A~~~~~  769 (787)
                      .||.+...
T Consensus        81 ~~a~~~~~   88 (90)
T d2cqia1          81 NWATTPSS   88 (90)
T ss_dssp             EECCCTTC
T ss_pred             EEcCCCCC
Confidence            99986653

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.7e-17  Score=135.55  Aligned_cols=80  Identities=18%  Similarity=0.264  Sum_probs=74.0

Q ss_pred             CcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCC--
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS--   85 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~--   85 (787)
                      ++..++|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||+|.++++|.+|++.||+..+.|  
T Consensus         3 s~k~~~lfV~n-----Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~   77 (85)
T d1fxla2           3 SIRDANLYVSG-----LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT   77 (85)
T ss_dssp             GGTTCEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCS
T ss_pred             CCCCCEEEEeC-----CCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCC
Confidence            45567899999     99999999999999999999999999987 69999999999999999999999999999998  


Q ss_pred             ceEEEEEc
Q psy3345          86 SRIKVEKC   93 (787)
Q Consensus        86 ~~i~v~~~   93 (787)
                      +.|.|.+|
T Consensus        78 ~~i~V~~A   85 (85)
T d1fxla2          78 EPITVKFA   85 (85)
T ss_dssp             SCCEEEEC
T ss_pred             EEEEEEeC
Confidence            45999876

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.4e-17  Score=138.01  Aligned_cols=80  Identities=18%  Similarity=0.346  Sum_probs=76.0

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      .+.+|+|.|     ||+++|++||+++|+.||.|.+|.++.++ .|+++|||||.|.++++|++|++.||+..|+|+.|.
T Consensus         4 ~~~kifV~n-----Lp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   78 (90)
T d1x5sa1           4 DEGKLFVGG-----LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   78 (90)
T ss_dssp             CCSEEEEES-----CCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCCEEEEEC-----CCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            356799999     99999999999999999999999999876 699999999999999999999999999999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|.+
T Consensus        79 V~~a~~   84 (90)
T d1x5sa1          79 VDQAGK   84 (90)
T ss_dssp             EEEEEC
T ss_pred             EEEcCC
Confidence            999987

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.3e-17  Score=134.27  Aligned_cols=76  Identities=33%  Similarity=0.534  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q psy3345         335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL  410 (787)
Q Consensus       335 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v  410 (787)
                      ++++|||+|||+++|+++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4568999999999999999999999999999999999989999999999999999999999999999999999987

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=4.5e-18  Score=135.67  Aligned_cols=76  Identities=24%  Similarity=0.422  Sum_probs=71.7

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      |+|||+|||+++|+++|+++|++||.|.+++|+++. .+|++||||||+|.++++|.+|++ +| +..++||+|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~~kG~aFV~f~~~~~a~~al~-~~-~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP-LTKRSRGFGFVTFMDQAGVDKVLA-QS-RHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCC-CSSSCSSEEEECCCCTTHHHHHHH-TT-TCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeeccc-CCCCccceEEEEECCHHHHHHHHH-cC-CCEECCeEEEEEEC
Confidence            689999999999999999999999999999999986 679999999999999999999997 55 79999999999987

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.2e-17  Score=140.06  Aligned_cols=85  Identities=26%  Similarity=0.429  Sum_probs=76.4

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCC-eeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-CeeecCceEEEEE
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-STHLYGRRLVLEW  763 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~-I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-~~~~~Gr~l~v~~  763 (787)
                      |+|||+|||..+|+++|+++|+.||. |.+++|+++...+|+++|||||+|.++++|..|++.|++ +..+.|++|.|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999995 999999988656799999999999999999999999863 4466799999999


Q ss_pred             ccccccH
Q psy3345         764 AEEADNV  770 (787)
Q Consensus       764 A~~~~~~  770 (787)
                      |+|+.+.
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9987653

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.1e-17  Score=141.01  Aligned_cols=81  Identities=19%  Similarity=0.391  Sum_probs=75.1

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      .++|||+|||+.+|+++|+++|+.||.|.+|+|+++. .+|+++|||||+|.+.++|.+|+. || +..|.|+.|.|.+|
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~-~tg~~kG~afV~F~~~e~a~~A~~-l~-g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR-NSRRSKGIAYVEFCEIQSVPLAIG-LT-GQRLLGVPIIVQAS   94 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC-CSSSCCCCEEEEESCGGGHHHHHH-HT-TEEETTEEEEEEEH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecC-CCccccceEEEEECCHHHHHHHHH-HC-CCEECCEEEEEEEC
Confidence            4689999999999999999999999999999999985 689999999999999999999995 86 79999999999999


Q ss_pred             cccc
Q psy3345         765 EEAD  768 (787)
Q Consensus       765 ~~~~  768 (787)
                      +++.
T Consensus        95 ~~~~   98 (101)
T d2cq4a1          95 QAEK   98 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
Confidence            7544

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.70  E-value=9.7e-18  Score=135.96  Aligned_cols=77  Identities=14%  Similarity=0.167  Sum_probs=67.6

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      .|+|.|     ||+++|++||+++|+.||.|..+.++.++ .|+++|||||.|.++++|++|++.||+..|+||.|.|.+
T Consensus         3 tl~v~n-----Lp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~   77 (81)
T d2ghpa1           3 TLWMTN-----FPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV   77 (81)
T ss_dssp             EEEEEC-----CCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             EEEEEC-----CCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            578888     99999999999999999999888887765 799999999999999999999999999999999999999


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      |+|
T Consensus        78 a~P   80 (81)
T d2ghpa1          78 SNP   80 (81)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            987

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3e-17  Score=133.49  Aligned_cols=77  Identities=21%  Similarity=0.346  Sum_probs=72.5

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ..+|+|.|     ||+++|++||+++|+.||.|.+|+|++++ +|+++|||||.|.++++|++||+. ++..|+||+|.|
T Consensus         6 ~~~lfV~n-----lp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~-~~~~i~Gr~i~V   79 (84)
T d1l3ka1           6 LRKLFIGG-----LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   79 (84)
T ss_dssp             GGEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CcEEEEEC-----CCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh-CCCEECCEEEEE
Confidence            45799999     99999999999999999999999999988 699999999999999999999985 999999999999


Q ss_pred             EEcc
Q psy3345          91 EKCS   94 (787)
Q Consensus        91 ~~~~   94 (787)
                      ..|.
T Consensus        80 ~~A~   83 (84)
T d1l3ka1          80 KRAV   83 (84)
T ss_dssp             EECC
T ss_pred             Eeee
Confidence            8874

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=2.2e-17  Score=135.23  Aligned_cols=80  Identities=28%  Similarity=0.519  Sum_probs=71.9

Q ss_pred             EEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCC--CCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS--GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       688 l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~--g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      |||+|||..+|+++|+++|++||.|.+++|+++....  +.++|||||+|.++++|.+|++.|| +..+.|++|.|+||+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~-~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQ-GHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHST-TCEETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhC-CCEECCEEEEEEECC
Confidence            7999999999999999999999999999998875222  2579999999999999999999997 699999999999997


Q ss_pred             ccc
Q psy3345         766 EAD  768 (787)
Q Consensus       766 ~~~  768 (787)
                      +..
T Consensus        80 ~~~   82 (85)
T d2cpfa1          80 RAT   82 (85)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3.3e-17  Score=139.11  Aligned_cols=83  Identities=25%  Similarity=0.454  Sum_probs=76.0

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||+.+|+++|+++|+.||.|.+|+|+++. .+|+++|||||+|.+.++|.+|++.+| + .+.||+|.|+
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~~kg~afV~f~~~~~A~~Ai~~~~-~-~l~Gr~l~V~   84 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR-QTGKSRGYGFVTMADRAAAERACKDPN-P-IIDGRKANVN   84 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS-SSCCCCSEEEEEESSHHHHHHHHTCSS-C-EETTEECEEE
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccc-cccccCCeEEEEECCHHHHHHHHHHCC-C-cCCCEEEEEE
Confidence            345789999999999999999999999999999999986 679999999999999999999999885 4 6999999999


Q ss_pred             Eccccc
Q psy3345         763 WAEEAD  768 (787)
Q Consensus       763 ~A~~~~  768 (787)
                      ||.+..
T Consensus        85 ~a~~~~   90 (103)
T d2cqda1          85 LAYLGA   90 (103)
T ss_dssp             ESTTTC
T ss_pred             EcCCCC
Confidence            998654

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=5.1e-17  Score=137.25  Aligned_cols=86  Identities=27%  Similarity=0.571  Sum_probs=78.7

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhc-----CCeeecCc
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC-----QSTHLYGR  757 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~-----~~~~~~Gr  757 (787)
                      ..+++|||+|||+.+|+++|+++|++||.|.+++++.+. .++.++|||||+|.+.++|.+||+.||     ++..+.||
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~-~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP-DTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeecccc-ccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            456789999999999999999999999999999998885 688899999999999999999999986     36789999


Q ss_pred             eEEEEEcccccc
Q psy3345         758 RLVLEWAEEADN  769 (787)
Q Consensus       758 ~l~v~~A~~~~~  769 (787)
                      +|+|+||.++++
T Consensus        85 ~l~v~~a~~k~~   96 (98)
T d1x4ha1          85 QLKVDLAVTRDE   96 (98)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCc
Confidence            999999998765

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=3e-17  Score=134.38  Aligned_cols=76  Identities=21%  Similarity=0.365  Sum_probs=69.8

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCC----CcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEG----KFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g----~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      |+|.|     ||+++|+++|+++|+.||.|.+|+|+.++++    +++|||||+|.++++|.+|++.||+..++||.|.|
T Consensus         1 LfV~n-----Lp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V   75 (85)
T d2cpfa1           1 LFIKN-----LNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   75 (85)
T ss_dssp             EEEES-----CCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CEEcC-----CCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            45666     9999999999999999999999999997732    47999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|.+
T Consensus        76 ~~a~~   80 (85)
T d2cpfa1          76 RISER   80 (85)
T ss_dssp             ECSSC
T ss_pred             EECCC
Confidence            99875

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.3e-17  Score=139.40  Aligned_cols=82  Identities=22%  Similarity=0.383  Sum_probs=76.1

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      .++|||+|||+.+|+++|+++|++||.|..+.|+++. .+++++|||||+|.+.++|.+||. ++ +..|.|+.|.|.+|
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~-~~~~~kg~aFV~f~~~~~a~~al~-~~-~~~l~G~~i~V~~a   96 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP-ASKRSRGFGFVTFSSMAEVDAAMA-AR-PHSIDGRVVEPKRA   96 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCT-TTSSCCSEEEEECSSHHHHHHHHT-SC-SEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccc-cCCCccCeEEEEECCHHHHHHHHH-hC-CCeECCEEEEEEEC
Confidence            4789999999999999999999999999999999986 678999999999999999999996 55 68999999999999


Q ss_pred             ccccc
Q psy3345         765 EEADN  769 (787)
Q Consensus       765 ~~~~~  769 (787)
                      .++++
T Consensus        97 ~~ke~  101 (103)
T d1x4ba1          97 VAREE  101 (103)
T ss_dssp             SSCCC
T ss_pred             cccCC
Confidence            98774

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=7.1e-18  Score=133.50  Aligned_cols=74  Identities=19%  Similarity=0.302  Sum_probs=69.4

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      +|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|++||+. ++..|+|+.|+|..
T Consensus         1 klfVgn-----Lp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGG-----LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEES-----CCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEEC
T ss_pred             CEEEcC-----CCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEE
Confidence            578888     99999999999999999999999999998 699999999999999999999986 88899999999976


Q ss_pred             c
Q psy3345          93 C   93 (787)
Q Consensus        93 ~   93 (787)
                      |
T Consensus        75 A   75 (75)
T d1x0fa1          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=5.7e-17  Score=131.80  Aligned_cols=78  Identities=24%  Similarity=0.465  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGK  414 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  414 (787)
                      .++|||+|||+++|+++|+++|+.||.|..+.|+.++.+|.++|||||+|.+.++|.+|++ +++..|.|+.|.|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            3589999999999999999999999999999999999999999999999999999999997 79999999999998764

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.68  E-value=2.2e-17  Score=135.21  Aligned_cols=80  Identities=18%  Similarity=0.299  Sum_probs=71.5

Q ss_pred             cccceEEEecCcccCCCccCC-HHHHHHHhhccCceEEEEEEecC--CCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345          10 VPRNHISLLDLDEVEFIYKIT-QEQLKAKFEEKGTVTDVQLKYTT--EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~-~~~l~~~f~~~g~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      +.+.+|+|.|     ||+++| |++|+++|+.||.|.+|+|+.+.  +|+++|||||.|.+.++|.+||+ ||+..|+||
T Consensus         2 ~e~~~l~V~n-----Lp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr   75 (86)
T d2ghpa3           2 LEGREIMIRN-----LSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNR   75 (86)
T ss_dssp             CTTTEEEEEE-----ECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCCEEEEEC-----CCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCE
Confidence            4577899999     999987 56699999999999999998753  79999999999999999999996 899999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|+|.+|++
T Consensus        76 ~l~V~~a~~   84 (86)
T d2ghpa3          76 EISVSLADK   84 (86)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEcCC
Confidence            999999986

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.68  E-value=9.6e-17  Score=144.87  Aligned_cols=79  Identities=19%  Similarity=0.333  Sum_probs=75.3

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ..+|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||.|.+.++|.+||+.||+..|+||.|.|
T Consensus        42 ~~~l~V~n-----Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V  116 (139)
T d1u6fa1          42 LRNLMVNY-----IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             TSEEEEES-----CSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCEEEEeC-----CCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34699999     99999999999999999999999999987 6999999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|.+
T Consensus       117 ~~a~~  121 (139)
T d1u6fa1         117 ALAAS  121 (139)
T ss_dssp             EESSC
T ss_pred             EEcCC
Confidence            99986

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.5e-17  Score=135.88  Aligned_cols=78  Identities=13%  Similarity=0.280  Sum_probs=73.1

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      ..+|+|.|     ||+++|+++|+++|+.||.|..|+|+.++ +.++|||||.|.+.++|++||+.|||..|+|+.|.|.
T Consensus         8 ~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~   81 (89)
T d1cvja2           8 VGNIFIKN-----LDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   81 (89)
T ss_dssp             TTEEEEES-----CCSSCCHHHHHHHHHTTSCEEEEEECCBT-TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEE
T ss_pred             CCEEEEeC-----CCCCCCHHHHHHHHHhcCCceEEEEEeec-CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34689999     99999999999999999999999999986 4588999999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +|++
T Consensus        82 ~a~~   85 (89)
T d1cvja2          82 RFKS   85 (89)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9986

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.8e-17  Score=140.22  Aligned_cols=78  Identities=26%  Similarity=0.450  Sum_probs=74.3

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      ..|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++ +|+++|||||+|.+.++|.+|++.||+..|+||.|.|.
T Consensus         9 rtl~V~n-----Lp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           9 RSVFVGN-----IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SCEEEES-----CCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CEEEEEC-----CCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3588888     99999999999999999999999999987 69999999999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +|.+
T Consensus        84 ~a~~   87 (104)
T d1p1ta_          84 NAAS   87 (104)
T ss_dssp             ETTC
T ss_pred             ECCC
Confidence            9875

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.3e-17  Score=138.16  Aligned_cols=81  Identities=12%  Similarity=0.179  Sum_probs=74.3

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      .......|+|+|     |||++||+||++||+.|| |..|+++++.+|+++|||||.|.+.++|++|++ +|+..|+||.
T Consensus        11 ~~~~~~~v~v~n-----Lp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~   83 (102)
T d1weza_          11 QSTTGHCVHMRG-----LPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRY   83 (102)
T ss_dssp             CCSSSCEEEEES-----CCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSC
T ss_pred             cCCCCCEEEEeC-----CCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEE
Confidence            344556799999     999999999999999998 468999999999999999999999999999997 6999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |+|.++.+
T Consensus        84 I~V~~s~~   91 (102)
T d1weza_          84 VELFLNST   91 (102)
T ss_dssp             CEEEEECC
T ss_pred             EEEEEcCC
Confidence            99999986

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=3.7e-17  Score=142.19  Aligned_cols=81  Identities=21%  Similarity=0.420  Sum_probs=74.2

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ...+++|||+|||..+|+++|+++|+.||.|.+|+++.+    +.++|||||+|.+.++|..|+..|| |..|.|++|.|
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~----~~~kG~afV~f~~~~~A~~Ai~~l~-g~~~~gr~l~V   78 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT----PETRGTAYVVYEDIFDAKNACDHLS-GFNVCNRYLVV   78 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS----TTTTTEEEEEESSHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc----CCcCCeEEEEECCHHHHHHHHHHhC-CCEECCEEEEE
Confidence            345789999999999999999999999999999999765    5679999999999999999999997 79999999999


Q ss_pred             EEcccc
Q psy3345         762 EWAEEA  767 (787)
Q Consensus       762 ~~A~~~  767 (787)
                      .||.+.
T Consensus        79 ~~a~~~   84 (114)
T d2f9da1          79 LYYNAN   84 (114)
T ss_dssp             EECCHH
T ss_pred             EEcCCC
Confidence            999743

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.4e-17  Score=138.91  Aligned_cols=78  Identities=14%  Similarity=0.266  Sum_probs=73.3

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ...|+|.|     ||+++|+++|+++|+.||.|.+|.|++++ +|+++|||||.|.++++|.+|++ ||+..|+|+.|.|
T Consensus        18 ~~tifV~n-----L~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V   91 (101)
T d2cq4a1          18 ARTVFCMQ-----LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIV   91 (101)
T ss_dssp             HTEEEEES-----CCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEE
T ss_pred             CCEEEEEC-----CCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            34599999     99999999999999999999999999987 69999999999999999999996 8999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|.+
T Consensus        92 ~~a~~   96 (101)
T d2cq4a1          92 QASQA   96 (101)
T ss_dssp             EEHHH
T ss_pred             EECCC
Confidence            99875

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.2e-17  Score=142.10  Aligned_cols=88  Identities=24%  Similarity=0.393  Sum_probs=80.4

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      .+..|+++|||+|||..+|+++|+++|+.||.|..+.++.+. .+|.++|||||+|.++++|.+|+..|| +..+.|++|
T Consensus        13 ~~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~-g~~~~g~~l   90 (102)
T d2cpxa1          13 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-MTGRMRGQAFITFPNKEIAWQALHLVN-GYKLYGKIL   90 (102)
T ss_dssp             CCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE-ECSSSCSEEEEECSSHHHHHHHHHHST-TCBCSSCBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeeccc-ccccccccceEEeccHHHHHHHHHHhC-CCEECCEEE
Confidence            345678999999999999999999999999999999887764 578999999999999999999999997 799999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      +|+||+++++
T Consensus        91 ~V~~ak~k~~  100 (102)
T d2cpxa1          91 VIEFGKNKKQ  100 (102)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEeCCCccc
Confidence            9999998765

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.9e-17  Score=129.14  Aligned_cols=75  Identities=24%  Similarity=0.503  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      +|||+|||+++|+++|+++|++||+|..+.++.++.+|+++|||||+|.+.++|.+|++ +++..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999999999999999999999999999999997 7999999999998653

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=3.9e-17  Score=134.00  Aligned_cols=77  Identities=19%  Similarity=0.267  Sum_probs=71.3

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEE-EEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ...|+|+|     ||+++|++||+++|+.||.|.+ +.+..+.+|+++|+|||.|.+.++|++|++.||+..|+||+|+|
T Consensus         9 ~~~l~v~n-----Lp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v   83 (86)
T d2cqpa1           9 PTIIKVQN-----MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   83 (86)
T ss_dssp             SEEEEEES-----CCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCEEEEEC-----CCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEE
Confidence            45689999     9999999999999999998866 67777779999999999999999999999999999999999999


Q ss_pred             EEc
Q psy3345          91 EKC   93 (787)
Q Consensus        91 ~~~   93 (787)
                      .+|
T Consensus        84 ~l~   86 (86)
T d2cqpa1          84 VLG   86 (86)
T ss_dssp             EES
T ss_pred             EEC
Confidence            875

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=6.7e-17  Score=134.97  Aligned_cols=78  Identities=21%  Similarity=0.408  Sum_probs=72.4

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||..+|+++|+++|++||.|.+|+|+++       +|||||+|.++++|..|+..|| +..+.|++|+|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-------kg~afV~f~~~~~A~~Ai~~l~-~~~i~g~~l~v~   87 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-------KGYSFVRFSTHESAAHAIVSVN-GTTIEGHVVKCY   87 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHT-TCEETTEECEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-------ceEEEEEECCHHHHHHHHHHhC-CCEECCEEEEEE
Confidence            34678999999999999999999999999999999876       7899999999999999999997 799999999999


Q ss_pred             Eccccc
Q psy3345         763 WAEEAD  768 (787)
Q Consensus       763 ~A~~~~  768 (787)
                      ||+++-
T Consensus        88 ~ak~~p   93 (96)
T d1x4ga1          88 WGKESP   93 (96)
T ss_dssp             CCCCCC
T ss_pred             EcCCCC
Confidence            998653

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=4.8e-17  Score=137.44  Aligned_cols=77  Identities=16%  Similarity=0.289  Sum_probs=73.0

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      .+|+|.|     ||+++|++||+++|+.||.|.+|+|+.++ +++++|||||.|.+.++|.+||+ +++..|+||.|.|.
T Consensus        21 ~~lfVgn-----Lp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~   94 (103)
T d1x4ba1          21 RKLFIGG-----LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPK   94 (103)
T ss_dssp             TEEEEEC-----CTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEE
T ss_pred             CEEEEeC-----CCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            5799999     99999999999999999999999999988 68999999999999999999997 59999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      .|.+
T Consensus        95 ~a~~   98 (103)
T d1x4ba1          95 RAVA   98 (103)
T ss_dssp             CCSS
T ss_pred             ECcc
Confidence            9987

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=7.2e-17  Score=131.41  Aligned_cols=78  Identities=23%  Similarity=0.395  Sum_probs=73.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeCCCC
Q psy3345         339 IFVRNLSYTVTEDDLTKLFEKYGPLAEV-ILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK  416 (787)
Q Consensus       339 l~V~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  416 (787)
                      |||+|||+++|+++|+++|++||.|.++ .+++++.+|+++|||||+|.+.++|.+|++.|+|..+.|++|+|.++.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999998764 78888889999999999999999999999999999999999999999865

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.5e-16  Score=130.13  Aligned_cols=81  Identities=22%  Similarity=0.371  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      .+.++|||+|||+++|+++|+++|+.||+|..|.++.+..+  .+|||||+|.+.++|.+|++.|+|..+.|+.|+|.++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45679999999999999999999999999999999988654  4789999999999999999999999999999999999


Q ss_pred             CCC
Q psy3345         414 KPK  416 (787)
Q Consensus       414 ~~~  416 (787)
                      .++
T Consensus        84 ~~~   86 (90)
T d2cqia1          84 TTP   86 (90)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            864

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.67  E-value=2.4e-16  Score=142.25  Aligned_cols=83  Identities=30%  Similarity=0.487  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      ...++|||+|||+++|+++|+++|+.||.|.+|.|++++.+|+++|||||+|.+.++|.+|++.|||..|+|+.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy3345         414 KPK  416 (787)
Q Consensus       414 ~~~  416 (787)
                      ..+
T Consensus       120 ~~~  122 (139)
T d1u6fa1         120 ASG  122 (139)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            865

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.66  E-value=1.5e-17  Score=137.47  Aligned_cols=81  Identities=17%  Similarity=0.329  Sum_probs=74.5

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||+.+|+++|+++|+.||.|.+++|+.+  .+|+++|||||+|.+.++|.+||+ || +..++|++|.|+
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~--~~g~~kg~afv~F~~~e~a~~Al~-~~-g~~~~g~~i~V~   86 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV--RTGTNRKFGYVDFESAEDLEKALE-LT-GLKVFGNEIKLE   86 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE--EEETTTTEEEEEESSHHHHHHHHH-GG-GEEETTEEEEEE
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec--CCCCccEEeEEeeCCHHHHHHHHh-cC-CcEECCEEEEEE
Confidence            35678999999999999999999999999999998766  589999999999999999999996 86 799999999999


Q ss_pred             Ecccc
Q psy3345         763 WAEEA  767 (787)
Q Consensus       763 ~A~~~  767 (787)
                      ||+.+
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99864

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.66  E-value=1.2e-17  Score=138.14  Aligned_cols=82  Identities=18%  Similarity=0.285  Sum_probs=75.5

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      ++..+..|+|.|     ||+++|+++|+++|+.||.|.++.|+.+++|+++|||||.|.+.++|++||+ ||+..|+||.
T Consensus         9 ~~~~~~~ifV~n-----L~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~   82 (91)
T d1fjeb1           9 ESTTPFNLFIGN-----LNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNE   82 (91)
T ss_dssp             SCSSSEEEEEEC-----CCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEE
T ss_pred             CCCCCcEEEEeC-----ccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEE
Confidence            334456799999     9999999999999999999999999887799999999999999999999996 8999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|+.
T Consensus        83 i~V~~ak~   90 (91)
T d1fjeb1          83 IKLEKPKG   90 (91)
T ss_dssp             EEEECCCC
T ss_pred             EEEEecCC
Confidence            99999975

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=4.9e-17  Score=129.76  Aligned_cols=74  Identities=22%  Similarity=0.357  Sum_probs=69.7

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      ||+|.|     ||+++||+||+++|+.||.|..+.++.++ .|+++|||||+|.+.++|++|++ +|+..|+||.|+|..
T Consensus         1 rlfV~n-----Lp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGG-----LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEEC-----CCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEE
T ss_pred             CEEEeC-----CCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEE
Confidence            577888     99999999999999999999999999988 68999999999999999999997 799999999999987


Q ss_pred             c
Q psy3345          93 C   93 (787)
Q Consensus        93 ~   93 (787)
                      |
T Consensus        75 A   75 (75)
T d2msta_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.4e-16  Score=128.37  Aligned_cols=75  Identities=20%  Similarity=0.290  Sum_probs=70.5

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      .+|+|.|     ||+++|++||+++|+.||.|..+.++.++ +|+++|||||.|.++++|.+|++ +|+..|+||.|+|.
T Consensus         3 r~lfV~n-----Lp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~   76 (79)
T d1l3ka2           3 KKIFVGG-----IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR   76 (79)
T ss_dssp             SEEEEEC-----CTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEE
T ss_pred             CEEEECC-----CCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            5788888     99999999999999999999999999988 78999999999999999999996 69999999999998


Q ss_pred             Ec
Q psy3345          92 KC   93 (787)
Q Consensus        92 ~~   93 (787)
                      .|
T Consensus        77 ~A   78 (79)
T d1l3ka2          77 KA   78 (79)
T ss_dssp             EC
T ss_pred             EC
Confidence            76

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.7e-16  Score=135.12  Aligned_cols=79  Identities=18%  Similarity=0.221  Sum_probs=70.9

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEE-EEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDV-QLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~   89 (787)
                      ....|+|+|     |||++|++||++||+.+|.|..+ .++.+.+|+++|||||.|.++++|++|++ +|+..|+||+|+
T Consensus        14 ~~~~v~v~n-----LP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~   87 (104)
T d1wg5a_          14 NDGFVRLRG-----LPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIE   87 (104)
T ss_dssp             CCCEEEEES-----CCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCE
T ss_pred             CCcEEEEeC-----CCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEE
Confidence            445699999     99999999999999999988774 44445589999999999999999999996 799999999999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.++.+
T Consensus        88 V~~~~~   93 (104)
T d1wg5a_          88 IFKSSR   93 (104)
T ss_dssp             EEEECT
T ss_pred             EEECCH
Confidence            999986

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2e-16  Score=132.14  Aligned_cols=81  Identities=23%  Similarity=0.415  Sum_probs=73.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ..+.++|||.|||+.+|+++|+++|+.||.|..+.+..+    +.++|||||+|.+.++|..||+.|| +..|.|++|+|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~----~~~~g~afV~f~~~e~a~~Ai~~l~-g~~~~g~~l~V   85 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR----RGGPPFAFVEFEDPRDAEDAVYGRD-GYDYDGYRLRV   85 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS----SSSSCCEEEEESCHHHHHHHHHHHT-TCEETTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc----ccccceEEEEECCHHHHHHHHHHhC-CCEECCEEEEE
Confidence            356789999999999999999999999999999998665    4578999999999999999999997 79999999999


Q ss_pred             EEcccc
Q psy3345         762 EWAEEA  767 (787)
Q Consensus       762 ~~A~~~  767 (787)
                      +||++.
T Consensus        86 ~~a~~~   91 (95)
T d1x4aa1          86 EFPRSG   91 (95)
T ss_dssp             ECCCCC
T ss_pred             EeccCC
Confidence            999864

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=5.9e-17  Score=128.15  Aligned_cols=75  Identities=24%  Similarity=0.397  Sum_probs=70.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       338 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      +|||+|||+++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|.+|++ +++..++|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 5778999999998754

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=5.6e-17  Score=137.20  Aligned_cols=83  Identities=20%  Similarity=0.393  Sum_probs=76.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ....++|||+|||..+|+++|+++|+.||.|.++++..+  .++.++|||||+|.+.++|.+|++.|| |..+.||++.|
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~--~~~~~~g~afV~f~~~~~A~~Ai~~ln-g~~i~gr~~~v   91 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD--SSGTSRGVGFARMESTEKCEAVIGHFN-GKFIKTPPGVS   91 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSCEEEEEEEEESCHHHHHHHHHHHB-TCCCCCCTTSC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc--cccccccceeEEeCCHHHHHHHHHHhC-CCEECCcCCcc
Confidence            345689999999999999999999999999999999887  488999999999999999999999997 79999999999


Q ss_pred             EEcccc
Q psy3345         762 EWAEEA  767 (787)
Q Consensus       762 ~~A~~~  767 (787)
                      .+++|-
T Consensus        92 ~~~~Pl   97 (101)
T d1x5oa1          92 APTEPL   97 (101)
T ss_dssp             CCSSCB
T ss_pred             CCCCCc
Confidence            998874

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.3e-16  Score=138.68  Aligned_cols=81  Identities=20%  Similarity=0.248  Sum_probs=74.4

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR   87 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   87 (787)
                      |+..+..|+|.|     ||+++|+++|+++|+.||.|.+|+|..  +|+++|||||+|.+.++|..|++.|||..|+||.
T Consensus         3 pp~~~r~l~V~n-----Lp~~~te~~l~~~F~~~G~v~~i~~~~--~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~   75 (114)
T d2f9da1           3 PPEVNRILYIRN-----LPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRY   75 (114)
T ss_dssp             CTTCCSEEEEES-----CCTTCCHHHHHHHHHTTSCEEEEEEEC--STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             ccCCCCEEEEEC-----CCCCCCHHHHHHHHhhcCCeEeecccc--cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            444566799999     999999999999999999999999976  4788999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.++.+
T Consensus        76 l~V~~a~~   83 (114)
T d2f9da1          76 LVVLYYNA   83 (114)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCC
Confidence            99999875

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.65  E-value=2.4e-16  Score=128.00  Aligned_cols=78  Identities=23%  Similarity=0.380  Sum_probs=70.8

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee-cCceEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL-YGRRLV  760 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~-~Gr~l~  760 (787)
                      .+|+++|||+|||..+|+++|+++|+.||.|.+++++++      .+|||||+|.+.++|..|++.|+ |..+ .|++|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~------~~g~afV~f~~~~~A~~A~~~l~-g~~~~~~~~i~   77 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN------RHDIAFVEFTTELQSNAAKEALQ-GFKITPTHAMK   77 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT------TCSCEEEEESSHHHHHHHHHHHT-TCBSSTTCBCE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc------cceeEEEecCCHHHHHHHHHHhC-CcEeCCCcEEE
Confidence            457889999999999999999999999999999999876      47899999999999999999997 5777 568999


Q ss_pred             EEEccc
Q psy3345         761 LEWAEE  766 (787)
Q Consensus       761 v~~A~~  766 (787)
                      |+||+.
T Consensus        78 v~~akk   83 (83)
T d2b0ga1          78 ITFAKK   83 (83)
T ss_dssp             EEECCC
T ss_pred             EEEecC
Confidence            999973

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=1e-16  Score=127.90  Aligned_cols=75  Identities=23%  Similarity=0.402  Sum_probs=70.5

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      +|||+|||+.+|+++|+++|+.||.|..+.++.+. .+|.++|||||+|.+.++|..|++ +| +..+.||+|.|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~-~~~~~~~~afV~F~~~~~a~~al~-~~-~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK-TTNRHRGFGFVTFESEDIVEKVCE-IH-FHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCT-TCTTSCCEEEEECSCHHHHHHHHH-CS-SCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec-cccccCceeEEEECCHHHHHHHHh-cC-CCEECCeEEEEEEC
Confidence            59999999999999999999999999999998875 678999999999999999999996 86 79999999999987

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.1e-16  Score=134.70  Aligned_cols=86  Identities=23%  Similarity=0.497  Sum_probs=76.0

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV  760 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~  760 (787)
                      +..+.++|||.|||+.+|+++|+++|+.|| |..++++.+...+|+++|||||+|.+.++|++|+ .|| +..+.||.|+
T Consensus        11 p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~-~~~~~gr~l~   87 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-EESLGNKRIR   87 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGG-TCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcC-CCEECCEEEE
Confidence            345678999999999999999999999999 8888888776568899999999999999998766 586 6999999999


Q ss_pred             EEEcccccc
Q psy3345         761 LEWAEEADN  769 (787)
Q Consensus       761 v~~A~~~~~  769 (787)
                      |+||.++..
T Consensus        88 V~~a~~~~~   96 (104)
T d1wi8a_          88 VDVADQAQD   96 (104)
T ss_dssp             EEECCCCCC
T ss_pred             EEECCCCCC
Confidence            999997654

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.3e-16  Score=126.14  Aligned_cols=77  Identities=23%  Similarity=0.358  Sum_probs=73.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEeeC
Q psy3345         336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPG  413 (787)
Q Consensus       336 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~~  413 (787)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.++++|.+|++ ++|..|+|+.|.|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4689999999999999999999999999999999999999999999999999999999996 8999999999999875

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.6e-16  Score=129.38  Aligned_cols=78  Identities=15%  Similarity=0.231  Sum_probs=73.2

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ....|+|.|     ||+++|++||+++|+.||.|.+|.|+.+++|+++|||||.|.++++|++||+ +++..++||.|.|
T Consensus         5 ~~rtvfV~n-----lp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v   78 (85)
T d1zh5a2           5 KNRSVYIKG-----FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLI   78 (85)
T ss_dssp             HTTEEEEEC-----CCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEE
T ss_pred             CcCEEEEEC-----CCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEE
Confidence            356799999     9999999999999999999999999999899999999999999999999997 5999999999999


Q ss_pred             EEcc
Q psy3345          91 EKCS   94 (787)
Q Consensus        91 ~~~~   94 (787)
                      .+..
T Consensus        79 ~~~~   82 (85)
T d1zh5a2          79 LFKD   82 (85)
T ss_dssp             EEGG
T ss_pred             EEcC
Confidence            8865

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.4e-16  Score=132.03  Aligned_cols=82  Identities=20%  Similarity=0.419  Sum_probs=73.7

Q ss_pred             CCCEEEEecCCccCcHHHHHH----HHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~----~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      |+++|||+|||..+|++||++    +|++||.|.+|++.+.    ++++|||||+|.+.++|.+|++.+| +..+.|++|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~----~~~~g~afV~F~~~~~A~~A~~~~~-~~~~~g~~l   76 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS----LKMRGQAFVIFKEVSSATNALRSMQ-GFPFYDKPM   76 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH----HHHTTCEEEEESSHHHHHHHHHHHT-TCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee----ccCCCceEEEECCHHHHHHHHHHhC-CCEECCEEE
Confidence            578999999999999999864    6899999999998653    6689999999999999999999997 799999999


Q ss_pred             EEEEccccccH
Q psy3345         760 VLEWAEEADNV  770 (787)
Q Consensus       760 ~v~~A~~~~~~  770 (787)
                      +|.||+++.+.
T Consensus        77 ~v~~ak~~~~~   87 (91)
T d1nu4a_          77 RIQYAKTDSDI   87 (91)
T ss_dssp             EEEECSSCCTH
T ss_pred             EEEEeCCCchh
Confidence            99999987754

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.6e-16  Score=133.59  Aligned_cols=85  Identities=19%  Similarity=0.287  Sum_probs=75.6

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCee--------EEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCee
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELK--------FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH  753 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~--------~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~  753 (787)
                      ....++|||.|||..+|+++|+++|+.||.|.        .+.++.+. .+|+++|||||+|.++++|.+||+.|| +..
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~-~~~~~~g~afV~f~~~~~a~~Ai~~l~-g~~   82 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK-ETGKPKGDATVSYEDPPTAKAAVEWFD-GKD   82 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT-TTCSBCSEEEEEBSSHHHHHHHHHHHT-TCE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeecc-ccccccceeeEEecCHHHHHHHHHHhC-CCE
Confidence            34678999999999999999999999999884        45566654 578999999999999999999999997 799


Q ss_pred             ecCceEEEEEccccc
Q psy3345         754 LYGRRLVLEWAEEAD  768 (787)
Q Consensus       754 ~~Gr~l~v~~A~~~~  768 (787)
                      ++||+|+|+||+++.
T Consensus        83 ~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          83 FQGSKLKVSLARKKP   97 (101)
T ss_dssp             ETTEECEEECSSCCC
T ss_pred             ECCEEEEEEEcCCCC
Confidence            999999999998764

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.2e-16  Score=135.20  Aligned_cols=80  Identities=11%  Similarity=0.239  Sum_probs=75.8

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ...+|+|.|     ||+++|+++|+++|+.||.|..+.++.+..|+++|||||.|.+.++|.+|++.|||..|.||.+.|
T Consensus        17 ~~~~lfV~n-----Lp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v   91 (101)
T d1x5oa1          17 DPTNLYISN-----LPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   91 (101)
T ss_dssp             CTTEEEEES-----CCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCcc
Confidence            456799999     999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .++.|
T Consensus        92 ~~~~P   96 (101)
T d1x5oa1          92 APTEP   96 (101)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            88776

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=1.8e-16  Score=129.43  Aligned_cols=78  Identities=28%  Similarity=0.483  Sum_probs=72.4

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||..+++++|+++|++||.|.+|++.++       +|||||+|.+.++|.+|++.|| +..+.|++|+|+|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-------k~~afV~f~~~~~A~~A~~~l~-g~~i~g~~l~V~~   78 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-------KGFGFIRLETRTLAEIAKVELD-NMPLRGKQLRVRF   78 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-------TTEEEEECSSSHHHHHHHHHHT-TCCBTTBCCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-------cceEEEEECCHHHHHHHHHHhC-CCEECCEEEEEEE
Confidence            4578999999999999999999999999999999875       6899999999999999999997 7999999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      |.+...
T Consensus        79 A~~~~~   84 (86)
T d2cpja1          79 ACHSAS   84 (86)
T ss_dssp             SSCCSC
T ss_pred             CCCcCC
Confidence            987653

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.7e-16  Score=128.11  Aligned_cols=77  Identities=14%  Similarity=0.274  Sum_probs=71.9

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      .++|||+|||..+|+++|+++|+.||.|.+|+|+++  .+|+++|||||+|.++++|.+||+ ++ +..+.|+.|.|.|+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~--~~~~~kG~afV~f~~~e~a~~al~-~~-~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKFVE-TP-GQKYKETDLLILFK   81 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC--TTCCEEEEEEEEESCHHHHHHHHT-CC-CCEETTEECEEEEG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee--ccCCcceEEEEEEcCHHHHHHHHH-HC-CCEECCEEEEEEEc
Confidence            468999999999999999999999999999999887  589999999999999999999996 55 79999999999997


Q ss_pred             c
Q psy3345         765 E  765 (787)
Q Consensus       765 ~  765 (787)
                      +
T Consensus        82 ~   82 (85)
T d1zh5a2          82 D   82 (85)
T ss_dssp             G
T ss_pred             C
Confidence            5

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=7.2e-17  Score=137.31  Aligned_cols=85  Identities=20%  Similarity=0.311  Sum_probs=79.9

Q ss_pred             CCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345           6 SGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus         6 ~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      ..|..|++.|+|.|     ||.++|+++|+++|+.||.|..+.++.+. +|+++|||||.|.++++|.+|++.||+..|.
T Consensus        12 ~~~~~ps~tl~V~n-----Lp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~   86 (102)
T d2cpxa1          12 YNPGEPNKVLYLKN-----LSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY   86 (102)
T ss_dssp             CCCCSCCSEEEEEC-----CCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCS
T ss_pred             CCCCCCCCEEEEeC-----CCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEEC
Confidence            44666788999999     99999999999999999999999998876 7999999999999999999999999999999


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      |+.|.|.+|++
T Consensus        87 g~~l~V~~ak~   97 (102)
T d2cpxa1          87 GKILVIEFGKN   97 (102)
T ss_dssp             SCBCEEEECCC
T ss_pred             CEEEEEEeCCC
Confidence            99999999987

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=9.5e-17  Score=129.23  Aligned_cols=76  Identities=20%  Similarity=0.325  Sum_probs=68.4

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCe-eecCceEEEEEc
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST-HLYGRRLVLEWA  764 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~-~~~Gr~l~v~~A  764 (787)
                      .+|||+|||..+|+++|+++|++||.|.++++.+.       +|||||+|.++++|.+|++.|| |. .+.|++|+|+||
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-------rg~aFV~f~~~~~A~~Ai~~ln-g~~~~~G~~i~V~~a   73 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-------SGYAFVDYPDQNWAIRAIETLS-GKVELHGKIMEVDYS   73 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-------TTEEEECCSCHHHHHHHHHHHT-TTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-------cceEEEEECCHHHHHHHHHHhC-CCeEECCEEEEEEEc
Confidence            46999999999999999999999999977766554       7999999999999999999997 55 699999999999


Q ss_pred             ccccc
Q psy3345         765 EEADN  769 (787)
Q Consensus       765 ~~~~~  769 (787)
                      .|+..
T Consensus        74 ~~k~~   78 (80)
T d2cqha1          74 VSKKL   78 (80)
T ss_dssp             CCCCC
T ss_pred             CCcCc
Confidence            98764

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=7.2e-16  Score=130.03  Aligned_cols=84  Identities=26%  Similarity=0.488  Sum_probs=77.9

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhC------CceeCCe
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD------GTVFLGR  406 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~------~~~~~g~  406 (787)
                      ..++++|||+|||+++|+++|+++|++||+|..+.++.+..++.++|||||+|.+.++|.+|++.|+      |..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3456799999999999999999999999999999999998889999999999999999999999886      6788999


Q ss_pred             EEEEeeCCCC
Q psy3345         407 MLHLIPGKPK  416 (787)
Q Consensus       407 ~l~v~~~~~~  416 (787)
                      .|.|.++.++
T Consensus        85 ~l~v~~a~~k   94 (98)
T d1x4ha1          85 QLKVDLAVTR   94 (98)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999999875

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.63  E-value=3.5e-16  Score=123.92  Aligned_cols=73  Identities=22%  Similarity=0.241  Sum_probs=67.4

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEc
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      .|+|.|     ||+++|+++|+++|+.||.|.+|+|+.++++. +|||||.|.++++|++||. +|+..|+|+.|.|..+
T Consensus         2 tv~V~n-----lp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           2 TVLVKN-----LPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             EEEEEE-----ECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             EEEEEC-----CCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            478888     99999999999999999999999999987655 5799999999999999996 6999999999999875

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=4.4e-16  Score=127.52  Aligned_cols=78  Identities=27%  Similarity=0.390  Sum_probs=71.2

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||..+|+++|+++|++||.|..+++.+       ++|||||+|.++++|.+|+..|| +..+.|+.|.|+|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-------~rg~afV~f~~~~~A~~Ai~~l~-~~~i~g~~i~V~~   78 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVEAMKALN-GKVLDGSPIEVTL   78 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-------CSSEEEEEESSHHHHHHHHHHHS-SEEETTEEEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-------ccEEEEEEeCCHHHHHHHHHHcC-CCEECCEEEEEEe
Confidence            457899999999999999999999999998877733       58999999999999999999997 7999999999999


Q ss_pred             cccccc
Q psy3345         764 AEEADN  769 (787)
Q Consensus       764 A~~~~~  769 (787)
                      |+|.+.
T Consensus        79 akP~~~   84 (86)
T d2cpda1          79 AKPVDK   84 (86)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            998764

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.8e-16  Score=126.18  Aligned_cols=74  Identities=19%  Similarity=0.296  Sum_probs=68.6

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      .+++|||+|+|  +|+++|+++|++||.|.++++.++       +|||||+|.+.++|..|+..|| +..+.|++|+|+|
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-------~~~afV~f~~~~~A~~Ai~~ln-g~~~~g~~l~V~~   73 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-------RNCAFVTYEKMESADQAVAELN-GTQVESVQLKVNI   73 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-------TTEEEEECSSHHHHHHHHHHHT-TCBCSSCBCEEEE
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-------CCEEEEEEcccHHHHHHHHHhC-CCEECCEEEEEEE
Confidence            56899999996  899999999999999999999765       6899999999999999999997 7999999999999


Q ss_pred             cccc
Q psy3345         764 AEEA  767 (787)
Q Consensus       764 A~~~  767 (787)
                      |+++
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            9864

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1.3e-16  Score=137.69  Aligned_cols=85  Identities=19%  Similarity=0.251  Sum_probs=75.0

Q ss_pred             CCCCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEE-EEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc
Q psy3345           5 LSGPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV   83 (787)
Q Consensus         5 ~~~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~-~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~   83 (787)
                      +..|.-+...|+|+|     |||++|++||++||+.||.|..+. +..+.+|+++|||||.|.+.++|++|++ ||+..|
T Consensus        11 ~~~~~~~~~~i~v~n-----Lp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i   84 (112)
T d1wela1          11 SRSPHEAGFCVYLKG-----LPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYM   84 (112)
T ss_dssp             CSSCCCCCCEEEEEC-----CCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCS
T ss_pred             CCCCCCCCeEEEEec-----CCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcC
Confidence            445666677899999     999999999999999999887654 4455699999999999999999999997 799999


Q ss_pred             CCceEEEEEccC
Q psy3345          84 FSSRIKVEKCSN   95 (787)
Q Consensus        84 ~~~~i~v~~~~~   95 (787)
                      +||+|+|..+.+
T Consensus        85 ~gR~i~V~~~~~   96 (112)
T d1wela1          85 GNRFIQVHPITK   96 (112)
T ss_dssp             TTSCBEEEEECH
T ss_pred             CCEEEEEEEcCh
Confidence            999999999875

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.6e-16  Score=132.61  Aligned_cols=81  Identities=22%  Similarity=0.387  Sum_probs=72.4

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC--CCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT--EGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      |..|...|+|.|     ||+++|++||+++|+.|| |.++.++.++  .|+++|||||+|.+.++|++|++ ||+..|+|
T Consensus        11 p~~p~~~v~V~n-----Lp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~g   83 (104)
T d1wi8a_          11 PKSPPYTAFLGN-----LPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGN   83 (104)
T ss_dssp             CSSSCEEEEEES-----CCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETT
T ss_pred             CCCCCCEEEEeC-----CCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECC
Confidence            333557899999     999999999999999999 7788888765  68999999999999999987775 79999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      |.|.|.+|.+
T Consensus        84 r~l~V~~a~~   93 (104)
T d1wi8a_          84 KRIRVDVADQ   93 (104)
T ss_dssp             EECEEEECCC
T ss_pred             EEEEEEECCC
Confidence            9999999986

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=3.3e-16  Score=135.52  Aligned_cols=76  Identities=33%  Similarity=0.498  Sum_probs=70.0

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||+.+|+++|+++|+.||.|..|.|++       ++|||||+|.+.++|.+||+.|| +..|.|++|+|+|
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-------~kg~afV~f~~~~~A~~A~~~ln-g~~~~gr~l~v~~   80 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-------GGITAIVEFLEPLEARKAFRHLA-YSKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-------SSSCEEEEESCHHHHHHHHHHHT-TCBSSSSBCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-------cCceEEEEEcCHHHHHHHHHHHc-CCccCCCeEEEEE
Confidence            457899999999999999999999999999998854       47999999999999999999997 7999999999999


Q ss_pred             cccc
Q psy3345         764 AEEA  767 (787)
Q Consensus       764 A~~~  767 (787)
                      |...
T Consensus        81 a~~~   84 (111)
T d1whxa_          81 APIG   84 (111)
T ss_dssp             EETT
T ss_pred             CCCC
Confidence            9743

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=6e-16  Score=131.26  Aligned_cols=80  Identities=21%  Similarity=0.312  Sum_probs=73.7

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceE--------EEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccC
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVT--------DVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNT   81 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~   81 (787)
                      ..+.|+|.|     ||+.+|++||++||+.||.|.        .+.+..++ .|+++|||||.|.++++|.+||+.||+.
T Consensus         7 ~~~~i~V~n-----Lp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           7 DNSAIYVQG-----LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCEEEEEC-----CCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEEC-----CCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            467899999     999999999999999999873        56777776 6999999999999999999999999999


Q ss_pred             ccCCceEEEEEccC
Q psy3345          82 YVFSSRIKVEKCSN   95 (787)
Q Consensus        82 ~~~~~~i~v~~~~~   95 (787)
                      .|+||.|.|.+|++
T Consensus        82 ~~~gr~i~V~~a~~   95 (101)
T d2cpea1          82 DFQGSKLKVSLARK   95 (101)
T ss_dssp             EETTEECEEECSSC
T ss_pred             EECCEEEEEEEcCC
Confidence            99999999999987

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=3.8e-16  Score=128.39  Aligned_cols=78  Identities=21%  Similarity=0.316  Sum_probs=70.4

Q ss_pred             CcccceEEEecCcccCCCccCCHHHH---HHHhhccCceEEEEEEecC-CCC---cceEEEEEecCHHHHHHHHHHhccC
Q psy3345           9 VVPRNHISLLDLDEVEFIYKITQEQL---KAKFEEKGTVTDVQLKYTT-EGK---FRRFAFIGYHREDQAQAALDYFNNT   81 (787)
Q Consensus         9 ~~~~~~~~~~~l~~~~lp~~~~~~~l---~~~f~~~g~i~~~~~~~~~-~g~---~~g~afv~f~~~~~a~~a~~~~~~~   81 (787)
                      ++.++.|+|.|     ||+++|++||   +++|++||.|.+|.|+.++ .+.   .+|||||+|.++++|.+|++.|||.
T Consensus         5 viq~n~vyV~n-----Lp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~   79 (89)
T d2cpia1           5 VVQKNLVFVVG-----LSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV   79 (89)
T ss_dssp             CCCSSCEEEEE-----ECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             EEecCEEEEEC-----CCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCC
Confidence            45677899999     9999999999   7789999999999999987 333   4599999999999999999999999


Q ss_pred             ccCCceEEEE
Q psy3345          82 YVFSSRIKVE   91 (787)
Q Consensus        82 ~~~~~~i~v~   91 (787)
                      .++||.|+|+
T Consensus        80 ~~~gr~lkvS   89 (89)
T d2cpia1          80 VVDGRTLKAS   89 (89)
T ss_dssp             EETTEEEEEE
T ss_pred             EECCEEEEEC
Confidence            9999999985

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.61  E-value=5.5e-16  Score=129.73  Aligned_cols=80  Identities=21%  Similarity=0.498  Sum_probs=72.3

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      .+.++|||+|||+.+|+++|+++|+.||.|..++.      +|.++|||||+|.+.++|..|+..|| +..+.|++|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~------~~~~~~~afV~f~~~~~A~~A~~~l~-~~~~~gr~i~V~   86 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ------DGKSKGIAYIEFKSEADAEKNLEEKQ-GAEIDGRSVSLY   86 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE------TTEEEEEEEEEESSHHHHHHHHHHTT-EEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee------cCccccEEEEEeCCHHHHHHHHHHcC-CCEECCEEEEEE
Confidence            35689999999999999999999999998866643      57789999999999999999999997 799999999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||.++..
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9998754

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=9.5e-16  Score=127.95  Aligned_cols=78  Identities=19%  Similarity=0.203  Sum_probs=71.8

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      +..+|+|.|     ||+++|++||+++|+.||.|..+.+..+  +.++|||||.|.+.++|..||+.||+..|.|++|.|
T Consensus        13 ~~~~l~V~n-----Lp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V   85 (95)
T d1x4aa1          13 NDCRIYVGN-----LPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   85 (95)
T ss_dssp             CSSEEEEES-----CCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEEC-----CCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            445699999     9999999999999999999999887654  567899999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      ++|++
T Consensus        86 ~~a~~   90 (95)
T d1x4aa1          86 EFPRS   90 (95)
T ss_dssp             ECCCC
T ss_pred             EeccC
Confidence            99986

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=5.8e-16  Score=126.39  Aligned_cols=75  Identities=20%  Similarity=0.304  Sum_probs=70.8

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      .+++|+|.|     ||+++|++||+++|+.||.|.+|++..+     +|||||+|.+.++|.+|++.||+..|+|+.|.|
T Consensus         7 ~~~~l~V~n-----Lp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V   76 (86)
T d2cpja1           7 QRSRLFVGN-----LPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   76 (86)
T ss_dssp             CTTEEEEES-----CCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CCCEEEEEC-----CCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            356799999     9999999999999999999999999865     689999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|.+
T Consensus        77 ~~A~~   81 (86)
T d2cpja1          77 RFACH   81 (86)
T ss_dssp             EESSC
T ss_pred             EECCC
Confidence            99986

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=6.1e-16  Score=126.74  Aligned_cols=79  Identities=24%  Similarity=0.351  Sum_probs=71.3

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeE-EEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~-v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      +..+.|||+|||+.++++||+++|+.||.|.. +.+..+  .+|+++|+|||+|.+.++|.+|++.|| +..+.||+|.|
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~--~~g~~~G~afV~f~~~e~a~~Ai~~l~-~~~l~gr~i~v   83 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EKGMPTGEAMVAFESRDEATAAVIDLN-DRPIGSRKVKL   83 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC--SSSCEEEEEEEEESCHHHHHHHHHHTT-TCEETTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC--CCCCcceEEEEEEcCcHHHHHHHHHcC-CCEECCEEEEE
Confidence            34567999999999999999999999999866 455555  589999999999999999999999997 79999999999


Q ss_pred             EEc
Q psy3345         762 EWA  764 (787)
Q Consensus       762 ~~A  764 (787)
                      ++|
T Consensus        84 ~l~   86 (86)
T d2cqpa1          84 VLG   86 (86)
T ss_dssp             EES
T ss_pred             EEC
Confidence            986

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=3e-16  Score=133.42  Aligned_cols=78  Identities=13%  Similarity=0.135  Sum_probs=71.1

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEE-EEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      +..|+|+|     |||++|++||++||+.||.|.. +.++.+.+|+++|||||.|.++++|++||+ +|+..|+||.|.|
T Consensus         8 ~~~v~v~n-----Lp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V   81 (103)
T d2cpya1           8 KVCAHITN-----IPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFV   81 (103)
T ss_dssp             CCEEEEES-----CCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEE
T ss_pred             ceEEEEeC-----CCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEE
Confidence            45599999     9999999999999999998876 666677799999999999999999999997 7999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .++.+
T Consensus        82 ~~~~~   86 (103)
T d2cpya1          82 HVVTL   86 (103)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98864

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.60  E-value=1.2e-15  Score=120.87  Aligned_cols=74  Identities=20%  Similarity=0.310  Sum_probs=67.2

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      ++|||+|||+.+++++|+++|+.||.|.+++|+.+.   +..+|||||+|.++++|.+|+. ++ +..++|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~---~~~~~~afV~F~~~~~a~~Al~-~~-~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL---KKNFRFARIEFARYDGALAAIT-KT-HKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT---TSSSEEEEEEESSHHHHHHHHT-TT-TCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeec---cccceEEEEEEcchHHhHHHHH-hc-CcEECCEEEEEEEC
Confidence            579999999999999999999999999999999883   3456899999999999999985 65 68999999999876

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.5e-15  Score=124.88  Aligned_cols=78  Identities=17%  Similarity=0.229  Sum_probs=69.2

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee-cCceEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL-YGRRLVL  761 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~-~Gr~l~v  761 (787)
                      +|+++|||+|||..+|+++|+++|++||.|..+.+...     .++|||||+|.+.++|.+|+..|+ +..+ .|+.|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~-----~~~~~afV~f~~~~~A~~A~~~l~-~~~i~~g~~l~v   81 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ-----KDRKMALIQMGSVEEAVQALIDLH-NHDLGENHHLRV   81 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS-----SSTTCEEEEESSHHHHHHHHHHHT-TCBSSSSCBCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee-----cccceeEEEECCHHHHHHHHHhcc-CCEecCCCEEEE
Confidence            46789999999999999999999999999988776543     357899999999999999999997 5766 5899999


Q ss_pred             EEccc
Q psy3345         762 EWAEE  766 (787)
Q Consensus       762 ~~A~~  766 (787)
                      +||++
T Consensus        82 ~~sk~   86 (88)
T d2adca2          82 SFSKS   86 (88)
T ss_dssp             EECSS
T ss_pred             EeCCC
Confidence            99975

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=3e-16  Score=123.77  Aligned_cols=69  Identities=13%  Similarity=0.201  Sum_probs=64.7

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC-CCCcceEEEEEecCHHHHHHHHHHhccCccCCceE
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI   88 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i   88 (787)
                      |+|.|     ||+++|+++|+++|+.||.|..++++.++ .|+++|+|||+|.+.++|++|++.|||..|+||.|
T Consensus         1 lyV~n-----Lp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRG-----LQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEES-----CCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeC-----CCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            45556     99999999999999999999999999987 78999999999999999999999999999999976

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.8e-15  Score=124.40  Aligned_cols=81  Identities=17%  Similarity=0.324  Sum_probs=72.9

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhc-CCeeecCceE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC-QSTHLYGRRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~-~~~~~~Gr~l  759 (787)
                      ...|+++|||+|||..+|+++|+++|++||.|.++++.++       +|+|||+|.+.++|.+|++.++ ++..+.|++|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEE
Confidence            3568899999999999999999999999999999998765       5899999999999999999764 3679999999


Q ss_pred             EEEEccccc
Q psy3345         760 VLEWAEEAD  768 (787)
Q Consensus       760 ~v~~A~~~~  768 (787)
                      +|+||+.++
T Consensus        77 ~v~~sk~~~   85 (88)
T d2cq1a1          77 YIQYSNHKE   85 (88)
T ss_dssp             EEEECSCSS
T ss_pred             EEEECCCCC
Confidence            999998654

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.1e-15  Score=131.52  Aligned_cols=76  Identities=21%  Similarity=0.338  Sum_probs=69.9

Q ss_pred             CCEEEEecCCc-cCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         685 GSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       685 ~~~l~V~nLp~-~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      .++|||.|||+ .+|+++|+++|+.||.|..|+|+++      .+|||||+|.++++|.+|++.|| +..|+|+.|.|+|
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~------~kg~afV~f~~~~~A~~ai~~ln-g~~l~g~~l~v~~   74 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN------KKENALVQMADGNQAQLAMSHLN-GHKLHGKPIRITL   74 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT------TSCCEEEEESCHHHHHHHHHHHT-TCBCSSSBCEEEC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec------ccceEEEEECCHHHHHHHHHHhC-CCEECCEEEEEEE
Confidence            57899999965 5999999999999999999999887      37999999999999999999997 7999999999999


Q ss_pred             cccc
Q psy3345         764 AEEA  767 (787)
Q Consensus       764 A~~~  767 (787)
                      |+..
T Consensus        75 s~~~   78 (109)
T d2adca1          75 SKHQ   78 (109)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            9743

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=2e-15  Score=119.43  Aligned_cols=72  Identities=24%  Similarity=0.456  Sum_probs=64.9

Q ss_pred             EEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcccc
Q psy3345         688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEA  767 (787)
Q Consensus       688 l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~~  767 (787)
                      |||+|||+++|+++|+++|++|| +..+++       ++++|||||.|.+.++|.+|++.|| +..+.|++|.|+||..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-------~~~~g~afv~f~~~~~A~~Ai~~ln-~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-------DKYKGTAFVTLLNGEQAEAAINTFH-QSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-------ETTTTEEEEEESSHHHHHHHHHHHT-TEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-------cccceeEEEEECCHHHHHHHHHHhC-CccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 655555       3358999999999999999999997 79999999999999765


Q ss_pred             c
Q psy3345         768 D  768 (787)
Q Consensus       768 ~  768 (787)
                      .
T Consensus        72 ~   72 (75)
T d1wi6a1          72 A   72 (75)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.4e-15  Score=126.89  Aligned_cols=75  Identities=12%  Similarity=0.203  Sum_probs=70.9

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      +...|+|.|     ||..+|+++|+++|+.||.|.+|+|+.+     +|||||.|.+.++|.+|+..||+..|+|+.|.|
T Consensus        17 ~~~~l~v~n-----L~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v   86 (96)
T d1x4ga1          17 KNCTVYCGG-----IASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC   86 (96)
T ss_dssp             SCCEEEEEC-----CSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEcC-----CCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            346799999     9999999999999999999999999976     799999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|++
T Consensus        87 ~~ak~   91 (96)
T d1x4ga1          87 YWGKE   91 (96)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99986

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=5.3e-16  Score=124.79  Aligned_cols=73  Identities=15%  Similarity=0.272  Sum_probs=67.0

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccC-ccCCceEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT-YVFSSRIKVE   91 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~-~~~~~~i~v~   91 (787)
                      ++|+|.|     ||+++|++||+++|+.||.|.++.+...     +|||||.|.++++|.+|++.|||. .|+|+.|.|.
T Consensus         2 n~l~V~n-----Lp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~   71 (80)
T d2cqha1           2 NKLYIGN-----LSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   71 (80)
T ss_dssp             CCEEEEC-----CCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CEEEEEC-----CCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEE
Confidence            4688888     9999999999999999999888777654     799999999999999999999997 4999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +|.|
T Consensus        72 ~a~~   75 (80)
T d2cqha1          72 YSVS   75 (80)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9987

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=2e-15  Score=126.38  Aligned_cols=80  Identities=18%  Similarity=0.351  Sum_probs=72.1

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecC--ce
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG--RR  758 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~G--r~  758 (787)
                      ...|.++|||.|||..+|+++|+++|++||.|..+++.++       ++||||+|.+.++|..|++.|| +..+.|  ++
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-------~~~afV~f~~~~~A~~A~~~l~-~~~i~g~~~~   84 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-------DSFAYIQYESLDAAQAACAKMR-GFPLGGPDRR   84 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-------SCCEEEEESSHHHHHHHHHHHT-TCBCSSSSCB
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-------ccEEEeccCCHHHHHHHHHHhC-CCEeCCCceE
Confidence            3457899999999999999999999999999999999765       6899999999999999999997 688877  58


Q ss_pred             EEEEEccccc
Q psy3345         759 LVLEWAEEAD  768 (787)
Q Consensus       759 l~v~~A~~~~  768 (787)
                      |+|+||+++.
T Consensus        85 l~v~~ak~~~   94 (97)
T d1whya_          85 LRVDFAKSGP   94 (97)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEeCCCCC
Confidence            9999998653

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=5.6e-16  Score=127.25  Aligned_cols=78  Identities=24%  Similarity=0.351  Sum_probs=70.3

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||+|||+.+|+++|+++|++||.|.+|+++.+      ++|||||+|.+.++|.+|+.  + +..+.|++|.|+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~------~~gfafV~f~~~~~a~~a~~--~-~~~i~g~~l~v~   73 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQIAQSLCG--E-DLIIKGISVHIS   73 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS------CCSCCEEECSCHHHHHHTTT--C-EEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec------cCceEEEEECCHHHHHHHHh--C-CCEECCEEeEEE
Confidence            35789999999999999999999999999999988665      68999999999999999985  4 688999999999


Q ss_pred             Ecccccc
Q psy3345         763 WAEEADN  769 (787)
Q Consensus       763 ~A~~~~~  769 (787)
                      ||.++++
T Consensus        74 ~a~~k~~   80 (88)
T d1wf0a_          74 NAEPKHN   80 (88)
T ss_dssp             CCCCCCC
T ss_pred             eCCCCCC
Confidence            9987664

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=8.7e-16  Score=126.19  Aligned_cols=77  Identities=21%  Similarity=0.327  Sum_probs=68.5

Q ss_pred             CCCEEEEecCCccCcHHHH---HHHHHhcCCeeEEEeccccCCCC---CCceEEEEEecCHHHHHHHHHHhcCCeeecCc
Q psy3345         684 TGSKILVRNIPFQAKQSEV---EELFKAFGELKFVRLPKKMVGSG---LHRGFGFVEFITKNEAKRAMKALCQSTHLYGR  757 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL---~~~F~~~G~I~~v~i~~~~~~~g---~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr  757 (787)
                      ..+.|||+|||+.+|+++|   +++|++||.|.+|.|+++. .++   .++|||||+|.++++|.+|++.|| |..++||
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~-~~~~~~~~~g~aFV~f~~~~~A~~Ai~~ln-g~~~~gr   84 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNST-SYAGSQGPSASAYVTYIRSEDALRAIQCVN-NVVVDGR   84 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCS-SCCSSSCCCEEEEEEESSHHHHHHHHHHHT-TEEETTE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeecc-CcCCCCCcceEEEEecccchhHHHHHHHhC-CCEECCE
Confidence            4567999999999999999   6789999999999999885 233   345999999999999999999997 7999999


Q ss_pred             eEEEE
Q psy3345         758 RLVLE  762 (787)
Q Consensus       758 ~l~v~  762 (787)
                      .|+|+
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99985

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.5e-15  Score=127.04  Aligned_cols=77  Identities=16%  Similarity=0.311  Sum_probs=70.2

Q ss_pred             CCCcccceEEEecCcccCCC-ccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345           7 GPVVPRNHISLLDLDEVEFI-YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .|....++|+|.|     || +.++++||+++|++||.|.+|+|       ++|||||.|.+.++|.+||+.||+..|+|
T Consensus        10 ~~~~~~~~lfV~n-----L~~~~~~~~~L~~~F~~~G~i~~~~i-------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (98)
T d1wf2a_          10 DPRSMNSRVFIGN-----LNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAG   77 (98)
T ss_dssp             CCSSCCCCEEEEE-----ECTTTCCHHHHHHSSTTSSCEEEEEE-------ETEEEEEEESSHHHHHHHHHTTTTCEETT
T ss_pred             CCCCCCcEEEEeC-----CCcccCCHHHHHHHHhhcCCEEEEEE-------eCCeEEEEECCHHHHHHHHHHcCCCEECC
Confidence            4445567899999     96 68899999999999999999998       37999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|++|++
T Consensus        78 ~~l~V~~a~~   87 (98)
T d1wf2a_          78 QVLDINLAAE   87 (98)
T ss_dssp             EECEEEETTS
T ss_pred             EEEEEEECCC
Confidence            9999999986

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.1e-15  Score=127.98  Aligned_cols=77  Identities=25%  Similarity=0.531  Sum_probs=69.1

Q ss_pred             cCCCCCEEEEecCC-ccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         681 AKQTGSKILVRNIP-FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp-~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      +....++|||.||| ..+++++|+++|++||.|.+++|         ++|||||+|.+.++|.+||+.|| +..+.|++|
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---------~rg~aFV~f~~~~~A~~Ai~~ln-g~~~~g~~l   80 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---------HKGFAFVQYVNERNARAAVAGED-GRMIAGQVL   80 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---------ETEEEEEEESSHHHHHHHHHTTT-TCEETTEEC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---------eCCeEEEEECCHHHHHHHHHHcC-CCEECCEEE
Confidence            34456789999996 57889999999999999999998         36899999999999999999997 799999999


Q ss_pred             EEEEcccc
Q psy3345         760 VLEWAEEA  767 (787)
Q Consensus       760 ~v~~A~~~  767 (787)
                      +|+||.+.
T Consensus        81 ~V~~a~~~   88 (98)
T d1wf2a_          81 DINLAAEP   88 (98)
T ss_dssp             EEEETTSC
T ss_pred             EEEECCCC
Confidence            99999864

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.1e-15  Score=125.35  Aligned_cols=76  Identities=24%  Similarity=0.461  Sum_probs=66.8

Q ss_pred             CCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEE
Q psy3345         684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW  763 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~  763 (787)
                      ..++|||+|||+.+|++||+++|++|| +..+.+.       .++|||||+|.++++|.+|++.|| +..+.|++|.|+|
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-------~~kg~afV~f~~~~~A~~Ai~~ln-~~~~~G~~l~V~~   74 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-------RNKRTAFVTLLNGEQAQNAIQMFH-QYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-------GGGTEEEECCSCHHHHHHHHHHHT-TEEETTEEEEEEE
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-------ccCCceEEEECCHHHHHHHHHHhC-CCEECCEEEEEEE
Confidence            457899999999999999999999999 4444443       358999999999999999999997 6999999999999


Q ss_pred             ccccc
Q psy3345         764 AEEAD  768 (787)
Q Consensus       764 A~~~~  768 (787)
                      |..+.
T Consensus        75 a~~~~   79 (88)
T d1wg1a_          75 QPTDA   79 (88)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98665

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=4.1e-16  Score=127.78  Aligned_cols=72  Identities=15%  Similarity=0.131  Sum_probs=67.5

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      ++|+|.|     ||+++|++||+++|+.||.|.+|+|+.+      |||||.|.+.++|++||+.||+..|+|+.|.|.+
T Consensus         1 nrvfV~n-----lp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~   69 (87)
T d3begb1           1 NRVVVSG-----LPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   69 (87)
T ss_dssp             CCEEEEE-----CCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CeEEEEC-----CCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeE
Confidence            5789999     9999999999999999999999998654      8999999999999999999999999999999988


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      +++
T Consensus        70 ~~~   72 (87)
T d3begb1          70 IRV   72 (87)
T ss_dssp             CEE
T ss_pred             Eec
Confidence            875

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=2e-15  Score=128.34  Aligned_cols=85  Identities=16%  Similarity=0.232  Sum_probs=76.8

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEee
Q psy3345         333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP  412 (787)
Q Consensus       333 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l~v~~  412 (787)
                      .....+|||+|||+++|+++|+++|+.+|.+..+.++.+..++.++|||||+|.+.++|++|++ +|+..|+||.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3456689999999999999999999999999887777777789999999999999999999996 899999999999999


Q ss_pred             CCCCCC
Q psy3345         413 GKPKEN  418 (787)
Q Consensus       413 ~~~~~~  418 (787)
                      +.+.+.
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            987643

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=7.5e-16  Score=127.46  Aligned_cols=78  Identities=21%  Similarity=0.337  Sum_probs=71.7

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHH----HhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKA----KFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~----~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      |+..|+|.|     ||+.+|++||++    +|+.||.|.+|++..  +|+++|||||.|.+.++|.+|++.||+..++|+
T Consensus         2 P~~tl~V~n-----Lp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~   74 (91)
T d1nu4a_           2 PNHTIYINN-----LNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   74 (91)
T ss_dssp             CCSEEEEES-----CCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCE
Confidence            577899999     999999999964    689999999988754  478999999999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy3345          87 RIKVEKCSN   95 (787)
Q Consensus        87 ~i~v~~~~~   95 (787)
                      .|.|.+|++
T Consensus        75 ~l~v~~ak~   83 (91)
T d1nu4a_          75 PMRIQYAKT   83 (91)
T ss_dssp             ECEEEECSS
T ss_pred             EEEEEEeCC
Confidence            999999986

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.58  E-value=3.1e-15  Score=121.27  Aligned_cols=78  Identities=21%  Similarity=0.321  Sum_probs=70.5

Q ss_pred             CCCCCeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc-CCe
Q psy3345         577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL-DEH  655 (787)
Q Consensus       577 ~~~~~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l-~g~  655 (787)
                      ..|.++|||+|||..+++++|.++|+.||.|.++++.++          .+|||||+|.+.++|..|+..|||..+ +|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----------~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   74 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----------RHDIAFVEFTTELQSNAAKEALQGFKITPTH   74 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----------TCSCEEEEESSHHHHHHHHHHHTTCBSSTTC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----------cceeEEEecCCHHHHHHHHHHhCCcEeCCCc
Confidence            456789999999999999999999999999999999753          358999999999999999999999888 579


Q ss_pred             EEEEEecCc
Q psy3345         656 QIELKRSNR  664 (787)
Q Consensus       656 ~l~v~~~~~  664 (787)
                      .|.|.|+.+
T Consensus        75 ~i~v~~akk   83 (83)
T d2b0ga1          75 AMKITFAKK   83 (83)
T ss_dssp             BCEEEECCC
T ss_pred             EEEEEEecC
Confidence            999999863

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=4.3e-16  Score=122.89  Aligned_cols=70  Identities=31%  Similarity=0.515  Sum_probs=67.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q psy3345         339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRML  408 (787)
Q Consensus       339 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~g~~l  408 (787)
                      |||+|||+++|+++|+++|++||+|..+.+..++.++.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            7999999999999999999999999999999998899999999999999999999999999999999876

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=5.7e-16  Score=126.89  Aligned_cols=74  Identities=16%  Similarity=0.352  Sum_probs=68.9

Q ss_pred             EEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEccc
Q psy3345         687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE  766 (787)
Q Consensus       687 ~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~~  766 (787)
                      +|||+|||+.+|+++|+++|+.||.|.+++|+++        |||||+|.+.++|.+||..|| +..|.|+.|.|.|+.+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~--------g~afV~f~~~~~a~~Ai~~l~-g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVEFVRKEDMTYAVRKLD-NTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--------SEEEEEESSHHHHHHHHHHHT-TCBCCCTTSCCCBCEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc--------ceeeEEeCCHHHHHHHHHHhC-CCEECCcEeEEeEEec
Confidence            6999999999999999999999999999998664        799999999999999999997 7999999999999986


Q ss_pred             ccc
Q psy3345         767 ADN  769 (787)
Q Consensus       767 ~~~  769 (787)
                      +..
T Consensus        73 ~~~   75 (87)
T d3begb1          73 KVD   75 (87)
T ss_dssp             EEC
T ss_pred             CcC
Confidence            654

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3e-15  Score=123.05  Aligned_cols=77  Identities=22%  Similarity=0.273  Sum_probs=69.7

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc-CCceEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV-FSSRIK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~-~~~~i~   89 (787)
                      |++.|+|.|     ||+++|+++|+++|+.||.|..+.+...   +++|||||.|.+.++|.+|+..|||..| +||.|+
T Consensus         9 Ps~tL~V~N-----Lp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~   80 (88)
T d2adca2           9 PSATLHLSN-----IPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR   80 (88)
T ss_dssp             SCSEEEEEC-----CCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCE
T ss_pred             CCCEEEEEC-----CCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEE
Confidence            567799999     9999999999999999999988877653   5689999999999999999999999887 699999


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.++++
T Consensus        81 v~~sk~   86 (88)
T d2adca2          81 VSFSKS   86 (88)
T ss_dssp             EEECSS
T ss_pred             EEeCCC
Confidence            999985

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.57  E-value=2.4e-15  Score=125.76  Aligned_cols=77  Identities=18%  Similarity=0.295  Sum_probs=70.3

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ++..|+|.|     ||+++|++||+++|+.||.|..+.    .+|+++|||||.|.+.++|.+|++.||+..|+||.|.|
T Consensus        15 ~~~~l~V~n-----L~~~~te~~l~~~F~~~g~v~~~~----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          15 AARTLLAKN-----LSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             GGGEEEEES-----CCSSCCHHHHHHHHCSEEEECCEE----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHhcccceeee----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            567799999     999999999999999999876553    36899999999999999999999999999999999999


Q ss_pred             EEccCC
Q psy3345          91 EKCSNL   96 (787)
Q Consensus        91 ~~~~~~   96 (787)
                      .+|.+.
T Consensus        86 ~~a~~k   91 (96)
T d1fjca_          86 YYTGEK   91 (96)
T ss_dssp             EECSSS
T ss_pred             EEeCCC
Confidence            999973

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.9e-15  Score=126.52  Aligned_cols=78  Identities=18%  Similarity=0.180  Sum_probs=70.5

Q ss_pred             eEEEecCcccCCCccCCHHHHHHHhhccCc-eEEEEEEecC--CCCcceEEEEEecCHHHHHHHHHHhccC--ccCCceE
Q psy3345          14 HISLLDLDEVEFIYKITQEQLKAKFEEKGT-VTDVQLKYTT--EGKFRRFAFIGYHREDQAQAALDYFNNT--YVFSSRI   88 (787)
Q Consensus        14 ~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~-i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~~~~~~--~~~~~~i   88 (787)
                      +|+|.|     ||+++|+++|+++|+.||. |.+|.|+.+.  .|+++|||||.|.++++|.+|++.|++.  .++|+.|
T Consensus         3 rLyV~n-----Lp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i   77 (96)
T d2disa1           3 RLFIGG-----IPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   77 (96)
T ss_dssp             EEEEEC-----CCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             EEEEcC-----CCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEE
Confidence            577888     9999999999999999995 9999999875  4889999999999999999999999754  5679999


Q ss_pred             EEEEccCC
Q psy3345          89 KVEKCSNL   96 (787)
Q Consensus        89 ~v~~~~~~   96 (787)
                      .|.+|+|.
T Consensus        78 ~V~~A~p~   85 (96)
T d2disa1          78 AVDWAEPE   85 (96)
T ss_dssp             EEEESCSS
T ss_pred             EEEEcCCC
Confidence            99999873

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=2.2e-15  Score=130.22  Aligned_cols=82  Identities=57%  Similarity=0.987  Sum_probs=76.2

Q ss_pred             hcCCCCEEEEeCCCCCCCHHHHHHhhccCCCeeEEEecCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeeEEEEEecCcc
Q psy3345         443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGV  522 (787)
Q Consensus       443 ~~~~~~~i~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~a~V~F~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~  522 (787)
                      ..+..++|+|+|||+.+++++|+++|+.||.|..|.|++.+++|||+|.+.++|.+|+..|||..|.|++|.|+|++...
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999997764


Q ss_pred             cc
Q psy3345         523 FA  524 (787)
Q Consensus       523 ~~  524 (787)
                      +.
T Consensus        86 ~~   87 (111)
T d1whxa_          86 FG   87 (111)
T ss_dssp             TC
T ss_pred             cc
Confidence            43

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.2e-15  Score=129.11  Aligned_cols=82  Identities=23%  Similarity=0.307  Sum_probs=73.5

Q ss_pred             CCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ...+.+|||+|||+++|++||+++|+.|| |..+.++.+  .+|+++|||||+|.+.++|++|++ +| +..|.||.|.|
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~--~~g~~~G~afVeF~~~~~a~~Al~-~~-~~~i~gR~I~V   86 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG--PDGRVTGEADVEFATHEDAVAAMA-KD-KANMQHRYVEL   86 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES--SSSCEEEEEEEECSSSHHHHHHHT-TS-SCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe--cCCcceEEEEEEECCHHHHHHHHH-cC-CCEECCEEEEE
Confidence            34567999999999999999999999998 567888887  479999999999999999999986 76 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      .|+.+..
T Consensus        87 ~~s~~~~   93 (102)
T d1weza_          87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EEcCCCC
Confidence            9998665

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.5e-15  Score=120.46  Aligned_cols=73  Identities=25%  Similarity=0.353  Sum_probs=67.7

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ..+.|+|.|     ||  +|+++|+++|+.||.|.+|.+..+     +|||||.|.+.++|..|++.||+..++|++|.|
T Consensus         4 ~~~ti~V~~-----~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V   71 (79)
T d2bz2a1           4 KGNTLYVYG-----ED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKV   71 (79)
T ss_dssp             CCCEEEEEC-----SS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCEEEEEC-----CC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEE
Confidence            456799999     86  899999999999999999999754     689999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+|++
T Consensus        72 ~~a~~   76 (79)
T d2bz2a1          72 NIARK   76 (79)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99986

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=7.8e-16  Score=131.87  Aligned_cols=80  Identities=14%  Similarity=0.212  Sum_probs=71.6

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee--cCceEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL--YGRRLV  760 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~--~Gr~l~  760 (787)
                      .+..+|||+|||+.+|+++|+++|++||.|.++.|+.+.     ++|+|||+|.++++|.+|+..|| +..+  .|++|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~-----~~g~aFV~f~~~e~A~~Ai~~ln-~~~l~~~~~~l~   78 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLD-GQNIYNACCTLR   78 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHH-SCCSSTTCCCCE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC-----CCCeEEEEECCHHHHHHHHHHHC-CCEeccCCcEEE
Confidence            356789999999999999999999999999999998763     58999999999999999999998 5777  478999


Q ss_pred             EEEccccc
Q psy3345         761 LEWAEEAD  768 (787)
Q Consensus       761 v~~A~~~~  768 (787)
                      |.|+++..
T Consensus        79 v~~s~~~~   86 (108)
T d2adba1          79 IDFSKLTS   86 (108)
T ss_dssp             EEECSSCS
T ss_pred             EEecCCcc
Confidence            99998654

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=3.2e-15  Score=125.01  Aligned_cols=77  Identities=17%  Similarity=0.375  Sum_probs=70.9

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE  762 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~  762 (787)
                      ...++|||.|||+.++++||+++|+.||.|.+++|.+        +|||||+|.+.++|.+||+.|| +..|.|+.|.|.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~--------~g~afV~f~~~~~a~~Ai~~ln-g~~~~g~~i~v~   83 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK--------DGMGMVEYLRKEDMEYALRKLD-DTKFRSHEGETS   83 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET--------TTEEEEEESSHHHHHHHHHHHS-SEEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc--------cceEEEEECCHHHHHHHHHHhC-CCEeCCeEEEEE
Confidence            4567899999999999999999999999999999864        3799999999999999999997 799999999999


Q ss_pred             Eccccc
Q psy3345         763 WAEEAD  768 (787)
Q Consensus       763 ~A~~~~  768 (787)
                      |++++.
T Consensus        84 ~~~~~~   89 (98)
T d1wg4a_          84 YIRVYP   89 (98)
T ss_dssp             EEEEEC
T ss_pred             EEecCC
Confidence            998654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.1e-15  Score=128.14  Aligned_cols=82  Identities=20%  Similarity=0.310  Sum_probs=72.4

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeE-EEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEE
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~-v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      ...++|||+|||+.+|+++|+++|+.||.|.. +.++.+  .+|+++|||||+|.++++|.+||. +| +..|.||.|.|
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~--~~g~~~G~afV~F~s~~~a~~Al~-~n-~~~i~gr~i~V   81 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--NNGQGLGQALVQFKNEDDARKSER-LH-RKKLNGREAFV   81 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC--TTSSCSSCEEEECSSHHHHHHHGG-GC-SEEETTEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeC--CCCCcCccEEEEECCHHHHHHHHh-cC-CCeECCcEEEE
Confidence            34678999999999999999999999998876 555555  589999999999999999999996 76 79999999999


Q ss_pred             EEccccc
Q psy3345         762 EWAEEAD  768 (787)
Q Consensus       762 ~~A~~~~  768 (787)
                      .++.+++
T Consensus        82 ~~~~~~~   88 (103)
T d2cpya1          82 HVVTLED   88 (103)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9997543

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=7.2e-15  Score=120.13  Aligned_cols=73  Identities=18%  Similarity=0.318  Sum_probs=67.5

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEE
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEK   92 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~   92 (787)
                      ..|+|.|     ||+++|++||+++|+.||.|..+.+.     +++|||||.|.++++|.+|+..||+..|+||.|.|.+
T Consensus         9 k~l~V~n-----Lp~~~te~~l~~~F~~~g~i~~~~~~-----~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~   78 (86)
T d2cpda1           9 KILYVRN-----LMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   78 (86)
T ss_dssp             CEEEEES-----CCTTCCHHHHHHHHHTTSTTCEEEEE-----ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CEEEEcC-----CCCCCCHHHHHHhhcccceeeeEEEc-----cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4588888     99999999999999999998887764     4589999999999999999999999999999999999


Q ss_pred             ccC
Q psy3345          93 CSN   95 (787)
Q Consensus        93 ~~~   95 (787)
                      |+|
T Consensus        79 akP   81 (86)
T d2cpda1          79 AKP   81 (86)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            987

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=4.5e-15  Score=121.64  Aligned_cols=81  Identities=14%  Similarity=0.235  Sum_probs=71.9

Q ss_pred             CCCCCEEEEecCCcc-CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhc-CCeeecCceE
Q psy3345         682 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC-QSTHLYGRRL  759 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~-~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~-~~~~~~Gr~l  759 (787)
                      ..++++|||+|||.. +|++||+++|++||.|.+++++++       +++|||+|.+.++|..|+..++ ++..+.|++|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            457889999999986 899999999999999999999876       5789999999999999999774 3678999999


Q ss_pred             EEEEcccccc
Q psy3345         760 VLEWAEEADN  769 (787)
Q Consensus       760 ~v~~A~~~~~  769 (787)
                      +|+||+...+
T Consensus        78 ~V~~s~~~~~   87 (89)
T d1x4da1          78 RVHLSQKYKR   87 (89)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEECCCccc
Confidence            9999986544

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=4.7e-15  Score=124.10  Aligned_cols=79  Identities=20%  Similarity=0.271  Sum_probs=73.0

Q ss_pred             CCCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC-
Q psy3345           7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS-   85 (787)
Q Consensus         7 ~~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~-   85 (787)
                      +...|++.|+|.|     ||+++|+++|+++|+.||.|..|++..+     ++||||.|.+.++|.+|++.||+..|+| 
T Consensus        12 g~~~Ps~tl~V~n-----Lp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~   81 (97)
T d1whya_          12 GKANPTTRLWVGG-----LGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGP   81 (97)
T ss_dssp             CCCCCCSCEEEEC-----CCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCCCCEEEEcC-----CCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCC
Confidence            5667889999999     9999999999999999999999998754     7899999999999999999999999987 


Q ss_pred             -ceEEEEEccC
Q psy3345          86 -SRIKVEKCSN   95 (787)
Q Consensus        86 -~~i~v~~~~~   95 (787)
                       ++|+|++|++
T Consensus        82 ~~~l~v~~ak~   92 (97)
T d1whya_          82 DRRLRVDFAKS   92 (97)
T ss_dssp             SCBCEEEECCC
T ss_pred             ceEEEEEeCCC
Confidence             5899999986

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=3.3e-15  Score=127.92  Aligned_cols=77  Identities=18%  Similarity=0.205  Sum_probs=70.2

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc--CCceE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV--FSSRI   88 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~--~~~~i   88 (787)
                      +..+|+|+|     ||+.+|+++|+++|+.||.|..|.|+.+   +++|+|||.|.++++|++|++.||+..|  +|++|
T Consensus         6 ~~~~v~V~N-----L~~~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l   77 (108)
T d2adba1           6 PVLRIIVEN-----LFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   77 (108)
T ss_dssp             CEEEEESCS-----CCSTTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCC
T ss_pred             CeEEEEEeC-----cCCCCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEE
Confidence            355688888     9999999999999999999999999986   4589999999999999999999999987  68899


Q ss_pred             EEEEccC
Q psy3345          89 KVEKCSN   95 (787)
Q Consensus        89 ~v~~~~~   95 (787)
                      .|.++++
T Consensus        78 ~v~~s~~   84 (108)
T d2adba1          78 RIDFSKL   84 (108)
T ss_dssp             EEEECSS
T ss_pred             EEEecCC
Confidence            9999876

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=3.6e-15  Score=122.13  Aligned_cols=73  Identities=14%  Similarity=0.178  Sum_probs=65.7

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      ++.|+|.|     ||+++|++||+++|+.|| +..+.+     ++++|||||.|.++++|++|++.||+..|+||.|.|+
T Consensus         5 s~~i~V~n-----Lp~~~t~~~l~~lF~~~G-~~~~~~-----~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~   73 (88)
T d1wg1a_           5 SSGILVKN-----LPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQ   73 (88)
T ss_dssp             CCCEEEES-----CCSSCCHHHHHHHTCSSC-CCCEEE-----EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCEEEEeC-----CCCccChHHHHHHHHhcC-ceeeee-----eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            56799999     999999999999999999 334444     3568999999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      +++.
T Consensus        74 ~a~~   77 (88)
T d1wg1a_          74 LQPT   77 (88)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9975

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=1.2e-14  Score=123.42  Aligned_cols=81  Identities=15%  Similarity=0.262  Sum_probs=72.0

Q ss_pred             cCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC-CeeecCceE
Q psy3345         681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ-STHLYGRRL  759 (787)
Q Consensus       681 ~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~-~~~~~Gr~l  759 (787)
                      ...++.+|||+|||..+|++||+++|++||.|..+++.+.       +|+|||+|.+.++|..|+..+++ +..+.|++|
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            3457889999999999999999999999999999999765       68999999999999999998852 457889999


Q ss_pred             EEEEccccc
Q psy3345         760 VLEWAEEAD  768 (787)
Q Consensus       760 ~v~~A~~~~  768 (787)
                      +|+||+.++
T Consensus        84 ~v~~s~~~~   92 (104)
T d1wexa_          84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEcCCCc
Confidence            999997544

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=4.1e-15  Score=124.37  Aligned_cols=73  Identities=15%  Similarity=0.154  Sum_probs=68.5

Q ss_pred             cceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEE
Q psy3345          12 RNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE   91 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~   91 (787)
                      ..+|+|.|     ||+++|++||+++|+.||.|..|+|..      +|||||.|.+.++|++||+.||+..|+||.|.|.
T Consensus        15 ~~~i~V~N-----lp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~   83 (98)
T d1wg4a_          15 DFRVLVSG-----LPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETS   83 (98)
T ss_dssp             SCEEEEEC-----CCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEE
T ss_pred             CCEEEEEC-----CCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44699999     999999999999999999999999864      4899999999999999999999999999999999


Q ss_pred             EccC
Q psy3345          92 KCSN   95 (787)
Q Consensus        92 ~~~~   95 (787)
                      ++++
T Consensus        84 ~~~~   87 (98)
T d1wg4a_          84 YIRV   87 (98)
T ss_dssp             EEEE
T ss_pred             EEec
Confidence            9986

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=1.4e-15  Score=131.08  Aligned_cols=91  Identities=21%  Similarity=0.277  Sum_probs=76.7

Q ss_pred             ccCCCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceE
Q psy3345         680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL  759 (787)
Q Consensus       680 ~~~~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l  759 (787)
                      .+..++++|||+|||+.+|++||+++|+.||.|..+.++.+. .+|.++|||||+|.+.++|.+|+. || +..|+||.|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~-~~g~~~G~afVeF~~~e~a~~al~-~~-~~~i~gR~i   89 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG-PNGKATGEGFVEFRNEADYKAALC-RH-KQYMGNRFI   89 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC-TTSSEEEEEEEEBSSSHHHHHHHT-SC-SBCSTTSCB
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecC-cccceeeEEEEEECCHHHHHHHHH-cC-CCcCCCEEE
Confidence            334567899999999999999999999999988664443332 589999999999999999999996 76 799999999


Q ss_pred             EEEEccccccHHHH
Q psy3345         760 VLEWAEEADNVEDI  773 (787)
Q Consensus       760 ~v~~A~~~~~~~~~  773 (787)
                      .|..|.+.+..+.+
T Consensus        90 ~V~~~~~~~~~~~~  103 (112)
T d1wela1          90 QVHPITKKGMLEKI  103 (112)
T ss_dssp             EEEEECHHHHHHHH
T ss_pred             EEEEcChHHHHHHH
Confidence            99999877754444

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=2e-15  Score=123.86  Aligned_cols=75  Identities=19%  Similarity=0.310  Sum_probs=68.4

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ++++|+|.|     ||+++||+||+++|+.||.|.+|+++.    .++|||||+|.+.++|++||.  ++..|+|+.|.|
T Consensus         4 ~s~~lfV~n-----Lp~~~te~~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v   72 (88)
T d1wf0a_           4 GSSGVFVGR-----CTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHI   72 (88)
T ss_dssp             CCCEEEEES-----CCSSSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEE
T ss_pred             CCCEEEEeC-----CCCCCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEE
Confidence            477899999     999999999999999999999998754    468999999999999999996  788999999999


Q ss_pred             EEccCC
Q psy3345          91 EKCSNL   96 (787)
Q Consensus        91 ~~~~~~   96 (787)
                      .+|.+.
T Consensus        73 ~~a~~k   78 (88)
T d1wf0a_          73 SNAEPK   78 (88)
T ss_dssp             ECCCCC
T ss_pred             EeCCCC
Confidence            999873

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.6e-15  Score=126.66  Aligned_cols=75  Identities=17%  Similarity=0.267  Sum_probs=69.2

Q ss_pred             cceEEEecCcccCCCc-cCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEE
Q psy3345          12 RNHISLLDLDEVEFIY-KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV   90 (787)
Q Consensus        12 ~~~~~~~~l~~~~lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v   90 (787)
                      ++.|+|.|     ||+ .+|+++|+++|+.||.|..|+|+.++    +|||||.|.++++|.+|++.||+..|.||.|.|
T Consensus         2 ~~~l~V~n-----L~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v   72 (109)
T d2adca1           2 NSVLLVSN-----LNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   72 (109)
T ss_dssp             CSEEEEES-----CCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCEEEEeC-----CCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            46788888     955 69999999999999999999999873    789999999999999999999999999999999


Q ss_pred             EEccC
Q psy3345          91 EKCSN   95 (787)
Q Consensus        91 ~~~~~   95 (787)
                      .+++.
T Consensus        73 ~~s~~   77 (109)
T d2adca1          73 TLSKH   77 (109)
T ss_dssp             ECCSC
T ss_pred             EECCC
Confidence            99875

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=5.4e-15  Score=123.98  Aligned_cols=80  Identities=21%  Similarity=0.341  Sum_probs=71.1

Q ss_pred             CCCCCEEEEecCCcc-CcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHH--hcCCeeecCce
Q psy3345         682 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA--LCQSTHLYGRR  758 (787)
Q Consensus       682 ~~~~~~l~V~nLp~~-~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~--l~~~~~~~Gr~  758 (787)
                      ..++++|||+|||.+ +|+++|+++|++||.|.+++++++       +|+|||+|.+.++|.+|++.  ++ +..++|++
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-------k~~afV~f~~~~~A~~Ai~~~~~~-~~~~~gr~   86 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-------KSQAFIEMETREDAMAMVDHCLKK-ALWFQGRC   86 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-------TTEEEEECSSHHHHHHHHHHHHHS-CCCSSSSC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-------CCcEEEEecchHHHHHHHHHHhcC-CceECCEE
Confidence            346789999999985 899999999999999999999775       68999999999999999984  44 67899999


Q ss_pred             EEEEEcccccc
Q psy3345         759 LVLEWAEEADN  769 (787)
Q Consensus       759 l~v~~A~~~~~  769 (787)
                      |.|+||+...+
T Consensus        87 l~V~~s~~~~~   97 (99)
T d1x4fa1          87 VKVDLSEKYKK   97 (99)
T ss_dssp             CEEEEECSCSS
T ss_pred             EEEEEcCCccc
Confidence            99999987654

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=1.3e-14  Score=114.67  Aligned_cols=70  Identities=16%  Similarity=0.263  Sum_probs=62.6

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEcc
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCS   94 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~   94 (787)
                      |+|.|     ||+++|++||+++|++|| +..+++     ++++|||||.|.+.++|.+|++.||+..++||.|.|++++
T Consensus         1 i~V~n-----Lp~~~t~~~l~~~F~~~g-~~~~~~-----~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRG-----LPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEEC-----CCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CEEeC-----CCCcCCHHHHHHHHhccc-ccceee-----cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            45666     999999999999999999 455544     4678999999999999999999999999999999999997


Q ss_pred             C
Q psy3345          95 N   95 (787)
Q Consensus        95 ~   95 (787)
                      .
T Consensus        70 ~   70 (75)
T d1wi6a1          70 T   70 (75)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.5e-15  Score=126.89  Aligned_cols=77  Identities=18%  Similarity=0.250  Sum_probs=71.1

Q ss_pred             EecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEc
Q psy3345          17 LLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        17 ~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      +.++.+.+++..++|++|+++|++||.|.+|+|+.+.+|+++|+|||.|.+.++|.+|++.|||..++||.|.|+++
T Consensus        27 ~~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          27 VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             cchHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34455555999999999999999999999999998889999999999999999999999999999999999999986

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=7.8e-14  Score=118.21  Aligned_cols=78  Identities=14%  Similarity=0.222  Sum_probs=70.3

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc--cCccCC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN--NTYVFS   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~--~~~~~~   85 (787)
                      ...|+..|+|+|     ||+.+||+||+++|+.||.|..|.|...     +|+|||.|.+.++|+.|++.|+  +..++|
T Consensus        11 ~~~ps~~l~v~n-----lp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g   80 (104)
T d1wexa_          11 KVSVSPVVHVRG-----LCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CCCCCSEEEEES-----CCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             cCCCCCEEEEeC-----CCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEee
Confidence            345788899999     9999999999999999999999998754     7899999999999999999885  457899


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+++.
T Consensus        81 ~~l~v~~s~~   90 (104)
T d1wexa_          81 QQAFFNYSTS   90 (104)
T ss_dssp             SBCEEEECSS
T ss_pred             EEEEEEEcCC
Confidence            9999999975

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=4e-14  Score=116.10  Aligned_cols=76  Identities=16%  Similarity=0.248  Sum_probs=69.8

Q ss_pred             cccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhc--cCccCCce
Q psy3345          10 VPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN--NTYVFSSR   87 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~--~~~~~~~~   87 (787)
                      .|+..|+|.|     ||+++|+++|+++|+.||.|.+|.++.+     +|+|||.|.+.++|.+|++.++  +..++||.
T Consensus         6 ~Ps~~l~V~n-----Lp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~   75 (88)
T d2cq1a1           6 APSRVLHIRK-----LPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQP   75 (88)
T ss_dssp             SCCSEEEEES-----CCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCEEEEeC-----CCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCE
Confidence            4788899999     9999999999999999999999998865     6899999999999999999764  67899999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+++.
T Consensus        76 l~v~~sk~   83 (88)
T d2cq1a1          76 IYIQYSNH   83 (88)
T ss_dssp             CEEEECSC
T ss_pred             EEEEECCC
Confidence            99999975

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=2.3e-14  Score=120.78  Aligned_cols=78  Identities=17%  Similarity=0.140  Sum_probs=69.5

Q ss_pred             CCCEEEEecCCccCc-----HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce
Q psy3345         684 TGSKILVRNIPFQAK-----QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR  758 (787)
Q Consensus       684 ~~~~l~V~nLp~~~t-----~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~  758 (787)
                      ..++|||.||+..+.     .++|+++|+.||.|.++++++.       +|+|||+|.++++|.+|+..|| |..|+|++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-------~~~afV~f~~~~~A~~Ai~~ln-g~~~~g~~   75 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-------FKRVRINFSNPLSAADARLRLH-KTEFLGKE   75 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-------TTEEEEECSSTTHHHHHHHTST-TSEETTEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-------CCEEEEEECCHHHHHHHHHHhc-ccccCCCE
Confidence            568899999999863     2569999999999999999764       6899999999999999999997 79999999


Q ss_pred             EEEEEcccccc
Q psy3345         759 LVLEWAEEADN  769 (787)
Q Consensus       759 l~v~~A~~~~~  769 (787)
                      |+|.||++...
T Consensus        76 l~v~~a~~~~~   86 (104)
T d1weya_          76 MKLYFAQTLHI   86 (104)
T ss_dssp             CEEECCCCSSC
T ss_pred             eEEeecccCCC
Confidence            99999986653

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=8.6e-14  Score=116.51  Aligned_cols=75  Identities=17%  Similarity=0.170  Sum_probs=67.9

Q ss_pred             ccceEEEecCcccCCCcc-CCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHH--hccCccCCce
Q psy3345          11 PRNHISLLDLDEVEFIYK-ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDY--FNNTYVFSSR   87 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~--~~~~~~~~~~   87 (787)
                      ++..|+|.|     ||+. +|+++|+++|+.||.|.+|.|+.+     +|+|||.|.+.++|.+|++.  +|+..|+||.
T Consensus        17 ~~~~l~v~n-----Lp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~   86 (99)
T d1x4fa1          17 LGRVIHLSN-----LPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRC   86 (99)
T ss_dssp             CCCEEEEES-----CCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             CCCEEEEeC-----CcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEE
Confidence            456799999     9985 899999999999999999999865     68999999999999999984  5788999999


Q ss_pred             EEEEEccC
Q psy3345          88 IKVEKCSN   95 (787)
Q Consensus        88 i~v~~~~~   95 (787)
                      |.|.+|+.
T Consensus        87 l~V~~s~~   94 (99)
T d1x4fa1          87 VKVDLSEK   94 (99)
T ss_dssp             CEEEEECS
T ss_pred             EEEEEcCC
Confidence            99999975

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1.7e-14  Score=121.58  Aligned_cols=76  Identities=16%  Similarity=0.194  Sum_probs=71.4

Q ss_pred             CEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEc
Q psy3345         686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA  764 (787)
Q Consensus       686 ~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A  764 (787)
                      +.++|++++..+++++|+++|++||.|.+|+|+++  .+|+++|+|||+|.+.++|.+|++.|| |+.+.||+|.|+|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~--~~~~~~G~~fV~f~~~~~A~~Ai~~ln-g~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN--LGDHLVGNVYVKFRREEDAEKAVIDLN-NRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS--SSSSSEEEEEEEESCHHHHHHHHHHHT-TCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC--CCCCEeeEEEEEEechhHHHHHHHHHC-CCEECCEEEEEEEC
Confidence            45788999999999999999999999999999988  589999999999999999999999997 79999999999985

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.5e-13  Score=112.34  Aligned_cols=78  Identities=26%  Similarity=0.353  Sum_probs=69.5

Q ss_pred             CCcccceEEEecCcccCCCcc-CCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHh--ccCccC
Q psy3345           8 PVVPRNHISLLDLDEVEFIYK-ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYF--NNTYVF   84 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~--~~~~~~   84 (787)
                      -.-++..|+|.|     ||.. +|++||.++|+.||.|.+|.|+.+     +++|||.|.+.++|..|++.|  ++..++
T Consensus         4 ~~~~sr~v~v~n-----l~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~   73 (89)
T d1x4da1           4 RVETRRVVHIMD-----FQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVF   73 (89)
T ss_dssp             CCCCCCEEEEES-----CCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCCcEEEEEC-----CCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccC
Confidence            345677799999     9986 899999999999999999999875     579999999999999999976  567899


Q ss_pred             CceEEEEEccC
Q psy3345          85 SSRIKVEKCSN   95 (787)
Q Consensus        85 ~~~i~v~~~~~   95 (787)
                      ||.|.|.+|+.
T Consensus        74 gr~l~V~~s~~   84 (89)
T d1x4da1          74 GKPVRVHLSQK   84 (89)
T ss_dssp             TEECEEEEECC
T ss_pred             CceEEEEECCC
Confidence            99999999985

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=8.5e-13  Score=110.14  Aligned_cols=82  Identities=16%  Similarity=0.313  Sum_probs=71.1

Q ss_pred             CCCCCEEEEecC--CccCc---------HHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcC
Q psy3345         682 KQTGSKILVRNI--PFQAK---------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ  750 (787)
Q Consensus       682 ~~~~~~l~V~nL--p~~~t---------~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~  750 (787)
                      ...+++|+|+||  |.++.         .+||++.|++||.|..|+++.+     .++|+|||+|.++++|.+|+..|| 
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~-----~~~G~~fV~f~~~e~A~~A~~~ln-   78 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR-----HPDGVASVSFRDPEEADYCIQTLD-   78 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT-----CTTCEEEEECSCHHHHHHHHHHST-
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC-----CCccEEEEEECCHHHHHHHHHHhC-
Confidence            346789999999  65532         3689999999999999998765     368999999999999999999997 


Q ss_pred             CeeecCceEEEEEcccccc
Q psy3345         751 STHLYGRRLVLEWAEEADN  769 (787)
Q Consensus       751 ~~~~~Gr~l~v~~A~~~~~  769 (787)
                      |+.+.||+|.|+|+.++.+
T Consensus        79 g~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          79 GRWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             TCEETTEECEEEECCSCCC
T ss_pred             CcEECCEEEEEEEeCCcCC
Confidence            7999999999999987754

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=1.2e-14  Score=120.03  Aligned_cols=76  Identities=14%  Similarity=0.281  Sum_probs=65.1

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEE------ecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCc
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLK------YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS   86 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~------~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~   86 (787)
                      .+|+|.|     ||+.+||+||+++|+.||.|.++.+.      ....++++|||||+|.++++|++|++ ||+..+.||
T Consensus         2 RrlyVgN-----Lp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr   75 (90)
T d1u2fa_           2 RRLYVGN-----IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQ   75 (90)
T ss_dssp             CEEEECS-----CCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSS
T ss_pred             CEEEEcC-----CCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCE
Confidence            3678888     99999999999999999987665553      22357899999999999999999995 899999999


Q ss_pred             eEEEEEcc
Q psy3345          87 RIKVEKCS   94 (787)
Q Consensus        87 ~i~v~~~~   94 (787)
                      .|+|..++
T Consensus        76 ~l~V~r~k   83 (90)
T d1u2fa_          76 SLKIRRPH   83 (90)
T ss_dssp             CCCCBCTT
T ss_pred             EEEECCCC
Confidence            99997544

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=1.2e-14  Score=119.95  Aligned_cols=82  Identities=17%  Similarity=0.324  Sum_probs=68.8

Q ss_pred             CeEEecCCCCCCCHHHHHHHHhhcCCeEEEEEeecCCCCCCCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Q psy3345         581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK  660 (787)
Q Consensus       581 ~~l~V~NLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~~~s~G~afV~F~~~e~A~~A~~~lng~~l~g~~l~v~  660 (787)
                      ++|||+|||+++|+++|+++|+.||.+..+.+..........++.++|||||+|.+.++|..|+. |||..+.|+.|.|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            68999999999999999999999998877766533211123457889999999999999999985 99999999999997


Q ss_pred             ecC
Q psy3345         661 RSN  663 (787)
Q Consensus       661 ~~~  663 (787)
                      .+.
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=5.9e-13  Score=114.31  Aligned_cols=74  Identities=22%  Similarity=0.329  Sum_probs=64.1

Q ss_pred             CCCEE-EEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCH-HHHHHHHHHhcCCeeecCceEEE
Q psy3345         684 TGSKI-LVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK-NEAKRAMKALCQSTHLYGRRLVL  761 (787)
Q Consensus       684 ~~~~l-~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~-~~A~~Al~~l~~~~~~~Gr~l~v  761 (787)
                      .++.| ||+|||..+|+++|+++|++||.|.+|+|+++       +|||||.|.++ ++|..|+..+| +..+.++.+.|
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-------kg~gfV~F~~~~~~A~~a~~~~~-~~~l~~~~~~v   80 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-------AKEGIILFKEKAKEALGKAKDAN-NGNLQLRNKEV   80 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-------CSEEEEEESSCHHHHHHHHHHTT-TSCBCTTSSSE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-------CceEEEEecCcHHHHHHHHHHhc-CCceecCceEE
Confidence            44555 89999999999999999999999999999875       79999999995 78999999997 68787777777


Q ss_pred             EEcc
Q psy3345         762 EWAE  765 (787)
Q Consensus       762 ~~A~  765 (787)
                      .|+.
T Consensus        81 ~~~~   84 (113)
T d1owxa_          81 TWEV   84 (113)
T ss_dssp             EEEE
T ss_pred             EEee
Confidence            6665

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.35  E-value=3.1e-13  Score=113.77  Aligned_cols=75  Identities=11%  Similarity=-0.000  Sum_probs=67.5

Q ss_pred             ccceEEEecCcccCCCccC-C----HHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCC
Q psy3345          11 PRNHISLLDLDEVEFIYKI-T----QEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS   85 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~-~----~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~   85 (787)
                      .+++|+|.|     |+..+ +    +++|+++|+.||.|.+++++.     ++|+|||.|.+.++|.+|++.|||..|+|
T Consensus         4 ~~~~L~v~n-----l~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g   73 (104)
T d1weya_           4 GSSGLIACV-----ANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLG   73 (104)
T ss_dssp             CCCEEEEEC-----CCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETT
T ss_pred             CCceEEEEe-----CCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCC
Confidence            467899999     88876 3    356999999999999999984     47899999999999999999999999999


Q ss_pred             ceEEEEEccC
Q psy3345          86 SRIKVEKCSN   95 (787)
Q Consensus        86 ~~i~v~~~~~   95 (787)
                      +.|.|.+|++
T Consensus        74 ~~l~v~~a~~   83 (104)
T d1weya_          74 KEMKLYFAQT   83 (104)
T ss_dssp             EECEEECCCC
T ss_pred             CEeEEeeccc
Confidence            9999999986

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=1.2e-12  Score=109.53  Aligned_cols=77  Identities=18%  Similarity=0.331  Sum_probs=64.4

Q ss_pred             cCCCCCEEEEec--CCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeee-cCc
Q psy3345         681 AKQTGSKILVRN--IPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL-YGR  757 (787)
Q Consensus       681 ~~~~~~~l~V~n--Lp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~-~Gr  757 (787)
                      ...|..+|+|.|  ||..+|+++|+++|++||.|..++++++       +|||||+|.+.++|.+|+..|| |..+ .|.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-------k~~aFV~f~~~e~A~~A~~~ln-g~~i~~~~   85 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-------KPYSFARYRTTEESKRAYVTLN-GKEVVDDL   85 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-------CSCEEEEESSHHHHHHHHHHTT-TCEEECTT
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-------ccEEEEEECCHHHHHHHHHHhC-CCCCCCCC
Confidence            346788999977  9999999999999999999999998776       6799999999999999999997 5655 443


Q ss_pred             ----eEEEEEcc
Q psy3345         758 ----RLVLEWAE  765 (787)
Q Consensus       758 ----~l~v~~A~  765 (787)
                          .+.++|++
T Consensus        86 ~~~i~~~~~~~~   97 (101)
T d2cq2a1          86 GQKITLYLNFVE   97 (101)
T ss_dssp             SCEEECEEEEES
T ss_pred             CcEEEEEEEeee
Confidence                34446554

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=1.9e-12  Score=108.26  Aligned_cols=75  Identities=15%  Similarity=0.232  Sum_probs=62.2

Q ss_pred             CCcccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCcc-CC-
Q psy3345           8 PVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV-FS-   85 (787)
Q Consensus         8 ~~~~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~-~~-   85 (787)
                      +..|+..++|.+   .|||+++|+++|+++|+.||.|++|.++.+     +|||||.|.+.++|.+|++.|||..| ++ 
T Consensus        14 ~~~pt~~l~V~n---g~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~~~~   85 (101)
T d2cq2a1          14 VSYATQSLVVAN---GGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDL   85 (101)
T ss_dssp             CSSCCSEEEEET---CTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             CCCCCceEEEEC---CCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCCCCC
Confidence            345566777743   449999999999999999999999988765     68999999999999999999999876 33 


Q ss_pred             -ceEEE
Q psy3345          86 -SRIKV   90 (787)
Q Consensus        86 -~~i~v   90 (787)
                       ..|.+
T Consensus        86 ~~~i~~   91 (101)
T d2cq2a1          86 GQKITL   91 (101)
T ss_dssp             SCEEEC
T ss_pred             CcEEEE
Confidence             45554

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=2e-12  Score=109.09  Aligned_cols=83  Identities=20%  Similarity=0.351  Sum_probs=70.4

Q ss_pred             CCCCEEEEecC--CccC--------cHHHHHHHHHhcCCeeEEEeccccCC-CCCCceEEEEEecCHHHHHHHHHHhcCC
Q psy3345         683 QTGSKILVRNI--PFQA--------KQSEVEELFKAFGELKFVRLPKKMVG-SGLHRGFGFVEFITKNEAKRAMKALCQS  751 (787)
Q Consensus       683 ~~~~~l~V~nL--p~~~--------t~~dL~~~F~~~G~I~~v~i~~~~~~-~g~~~g~afV~F~~~~~A~~Al~~l~~~  751 (787)
                      .|++.|.|+||  |.++        ..+||++.|++||.|.+|.|+++... .....|++||.|.+.++|.+|+..|+ |
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~-G   80 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT-G   80 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHS-S
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHC-C
Confidence            57889999999  4443        34679999999999999999886411 23456899999999999999999997 7


Q ss_pred             eeecCceEEEEEccc
Q psy3345         752 THLYGRRLVLEWAEE  766 (787)
Q Consensus       752 ~~~~Gr~l~v~~A~~  766 (787)
                      +.+.||.|.+.|+.+
T Consensus        81 r~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          81 RKFANRVVVTKYCDP   95 (104)
T ss_dssp             CCSSSSCCEEEEECH
T ss_pred             CEECCeEEEEEEcCH
Confidence            999999999999975

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.28  E-value=3e-12  Score=101.80  Aligned_cols=73  Identities=19%  Similarity=0.269  Sum_probs=62.5

Q ss_pred             ccceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCce-EE
Q psy3345          11 PRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR-IK   89 (787)
Q Consensus        11 ~~~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~-i~   89 (787)
                      ....|.|.|     ||+++|++.| ++|+.||.|.++++.     +.+|||||.|.++++|++||+ +||..|+||. |.
T Consensus         3 ~~~wV~V~G-----~p~~~~~~il-~~F~~~G~I~~~~~~-----~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vg   70 (81)
T d1wwha1           3 DDTWVTVFG-----FPQASASYIL-LQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIG   70 (81)
T ss_dssp             GGGEEEEEC-----CCGGGHHHHH-HHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECE
T ss_pred             cccEEEEEC-----CChHHHHHHH-HHHHhhhhhheEEec-----CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEE
Confidence            355688888     9999997655 589999999999874     457999999999999999997 6999999984 67


Q ss_pred             EEEccC
Q psy3345          90 VEKCSN   95 (787)
Q Consensus        90 v~~~~~   95 (787)
                      |.+|..
T Consensus        71 V~~~~~   76 (81)
T d1wwha1          71 VKPCID   76 (81)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            998875

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=2.2e-12  Score=108.87  Aligned_cols=80  Identities=14%  Similarity=0.262  Sum_probs=69.7

Q ss_pred             ccceEEEecCcccCC----------CccCCHHHHHHHhhccCceEEEEEEecCCC---CcceEEEEEecCHHHHHHHHHH
Q psy3345          11 PRNHISLLDLDEVEF----------IYKITQEQLKAKFEEKGTVTDVQLKYTTEG---KFRRFAFIGYHREDQAQAALDY   77 (787)
Q Consensus        11 ~~~~~~~~~l~~~~l----------p~~~~~~~l~~~f~~~g~i~~~~~~~~~~g---~~~g~afv~f~~~~~a~~a~~~   77 (787)
                      |+..|.|+|     |          .+....+||++.|++||.|.+|.|+++.++   ...|+|||.|.++++|.+|++.
T Consensus         3 Ps~vl~l~N-----~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~   77 (104)
T d1o0pa_           3 PTEVLCLMN-----MVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG   77 (104)
T ss_dssp             CCSEEEEES-----SCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHH
T ss_pred             CCcEEEEeC-----CCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHH
Confidence            577788899     6          344456789999999999999999987644   3569999999999999999999


Q ss_pred             hccCccCCceEEEEEccC
Q psy3345          78 FNNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        78 ~~~~~~~~~~i~v~~~~~   95 (787)
                      |||..++||.|.|.++.+
T Consensus        78 l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          78 LTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HSSCCSSSSCCEEEEECH
T ss_pred             HCCCEECCeEEEEEEcCH
Confidence            999999999999999875

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=6e-12  Score=104.86  Aligned_cols=78  Identities=9%  Similarity=0.175  Sum_probs=67.7

Q ss_pred             cccceEEEecCcccCC--CccC---------CHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHh
Q psy3345          10 VPRNHISLLDLDEVEF--IYKI---------TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYF   78 (787)
Q Consensus        10 ~~~~~~~~~~l~~~~l--p~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~   78 (787)
                      -.+..|+|+|     |  |..+         .++||++.|++||.|..|++..+   ..+|+|||.|.++++|.+|++.|
T Consensus         6 ~~~r~v~l~n-----mf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~l   77 (99)
T d2dita1           6 RHERVVIIKN-----MFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTL   77 (99)
T ss_dssp             CSCCEEEEES-----SCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCccEEEEcc-----CCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHh
Confidence            3456688999     7  6543         34789999999999999988765   56799999999999999999999


Q ss_pred             ccCccCCceEEEEEccC
Q psy3345          79 NNTYVFSSRIKVEKCSN   95 (787)
Q Consensus        79 ~~~~~~~~~i~v~~~~~   95 (787)
                      ||..|+||.|.|+++.+
T Consensus        78 ng~~~~gr~i~v~~~~g   94 (99)
T d2dita1          78 DGRWFGGRQITAQAWDG   94 (99)
T ss_dssp             TTCEETTEECEEEECCS
T ss_pred             CCcEECCEEEEEEEeCC
Confidence            99999999999999876

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.25  E-value=6e-12  Score=100.01  Aligned_cols=74  Identities=9%  Similarity=0.126  Sum_probs=62.7

Q ss_pred             CCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCce-EEEEE
Q psy3345         685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR-LVLEW  763 (787)
Q Consensus       685 ~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~-l~v~~  763 (787)
                      .+.|+|.++|++++++ ++++|++||.|.++++.+.       +|||||+|.++++|.+||+ +| |..+.|+. |.|.-
T Consensus         4 ~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~~~-------~~~~fV~f~~~~~A~~Al~-~n-G~~~~g~~~vgV~~   73 (81)
T d1wwha1           4 DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSNT-------GNWMHIRYQSKLQARKALS-KD-GRIFGESIMIGVKP   73 (81)
T ss_dssp             GGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEECSS-------SSEEEEEESSHHHHHHHHT-TT-TCEETTTEECEEEE
T ss_pred             ccEEEEECCChHHHHH-HHHHHHhhhhhheEEecCC-------CCEEEEEEcccHHHHHHHh-cC-CCeECCcEEEEEEe
Confidence            4679999999999965 5568999999999987544       7999999999999999996 76 79999985 45888


Q ss_pred             ccccc
Q psy3345         764 AEEAD  768 (787)
Q Consensus       764 A~~~~  768 (787)
                      +..++
T Consensus        74 ~~~k~   78 (81)
T d1wwha1          74 CIDKN   78 (81)
T ss_dssp             CCCHH
T ss_pred             CCChh
Confidence            87654

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=1.1e-11  Score=106.12  Aligned_cols=71  Identities=14%  Similarity=0.047  Sum_probs=63.1

Q ss_pred             EEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCH-HHHHHHHHHhccCccCCceEEEEEc
Q psy3345          15 ISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHRE-DQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        15 ~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~-~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      ++|.|     ||+.+|+++|+++|+.||+|.+|.|+.+     +|||||.|.++ ++|..|+..+|+..+.++.+.|.++
T Consensus        14 ~fvgn-----L~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          14 KFSGD-----LDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             EEEES-----CCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             EEECC-----CCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            46677     9999999999999999999999999864     79999999996 7899999999999888887777776


Q ss_pred             cC
Q psy3345          94 SN   95 (787)
Q Consensus        94 ~~   95 (787)
                      ..
T Consensus        84 ~~   85 (113)
T d1owxa_          84 VL   85 (113)
T ss_dssp             EC
T ss_pred             ec
Confidence            54

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.54  E-value=0.00017  Score=52.33  Aligned_cols=65  Identities=20%  Similarity=0.308  Sum_probs=55.8

Q ss_pred             cCCHHHHH----HHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEcc
Q psy3345          28 KITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCS   94 (787)
Q Consensus        28 ~~~~~~l~----~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~~   94 (787)
                      .+.+++|+    ..|+++|.|..|.|....+|..  .|-|...+.+||.-|+..||+..|++++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34455555    6789999999999988767754  69999999999999999999999999999999886

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.47  E-value=0.00042  Score=50.18  Aligned_cols=60  Identities=18%  Similarity=0.232  Sum_probs=51.7

Q ss_pred             HHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhcCCeeecCceEEEEEcc
Q psy3345         701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE  765 (787)
Q Consensus       701 dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~~~~~~~Gr~l~v~~A~  765 (787)
                      -|.+.|.++|.|.++.|...  ..|..  .|-|...+.++|.-|+..|. .+.+++++|.|+|+.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~--~dg~~--~A~V~v~~~q~A~~~v~~Lh-R~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPH--TDYQL--KAVVQMENLQDAIGAVNSLH-RYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSC--CSTTC--CEEEEESSHHHHHHHHHHHT-TEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEec--cCCcE--EEEEEcCCHHHHHHHHHHHH-HHhcCCeEEEEEEec
Confidence            36778999999999998665  34544  59999999999999999995 799999999999985

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.32  E-value=0.00043  Score=54.12  Aligned_cols=67  Identities=12%  Similarity=0.152  Sum_probs=57.2

Q ss_pred             ceEEEecCcccCCCccCCHHHHHHHhhccCceEEEEEEecC--CC-CcceEEEEEecCHHHHHHHHHHhccCccC
Q psy3345          13 NHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTT--EG-KFRRFAFIGYHREDQAQAALDYFNNTYVF   84 (787)
Q Consensus        13 ~~~~~~~l~~~~lp~~~~~~~l~~~f~~~g~i~~~~~~~~~--~g-~~~g~afv~f~~~~~a~~a~~~~~~~~~~   84 (787)
                      ++|.||.     ||+++||+++.+.++..|.++-......+  .+ ....-|||.|.+.++.....+.++|..+.
T Consensus         2 tKvVvRr-----LPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRR-----LPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEE-----ECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEec-----CCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            5799999     99999999999999999998877777644  22 23478999999999999999999998653

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.99  E-value=0.001  Score=51.95  Aligned_cols=68  Identities=19%  Similarity=0.225  Sum_probs=56.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEecCCCCCC--cceEEEEEEcCHHHHHHHHHHhCCceeC
Q psy3345         337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK--TKGFALVTFLMPEHATQAYQHLDGTVFL  404 (787)
Q Consensus       337 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~--~~g~afV~F~~~~~A~~a~~~l~~~~~~  404 (787)
                      ++|.||.||+.+|++++.+.++..|.+........+.+.+  .-.-|||.|.+.++...-.+..+|..+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4799999999999999999999999888877766544432  2246999999999999999999998773

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.83  E-value=0.0025  Score=48.59  Aligned_cols=72  Identities=24%  Similarity=0.292  Sum_probs=56.8

Q ss_pred             CCCCeEEEcCCCCCCCH---------HHHHHHHHhcCCeeEEEEecCCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q psy3345         334 AESGRIFVRNLSYTVTE---------DDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFL  404 (787)
Q Consensus       334 ~~~~~l~V~nLp~~~te---------~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~F~~~~~A~~a~~~l~~~~~~  404 (787)
                      ++..+|.|.=...+..+         .+|.+.|..||.|.-++++.+        ..+|+|.+-+.|.+|++ ++|..+.
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~   83 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEc
Confidence            34456777544433322         467888999999999998765        58999999999999997 9999999


Q ss_pred             CeEEEEeeCC
Q psy3345         405 GRMLHLIPGK  414 (787)
Q Consensus       405 g~~l~v~~~~  414 (787)
                      |+.|.|....
T Consensus        84 G~~l~It~~~   93 (95)
T d1ufwa_          84 GRAVKISGPS   93 (95)
T ss_dssp             TEEEEEECCC
T ss_pred             ceEEEEecCC
Confidence            9999997643

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.29  E-value=0.0063  Score=46.34  Aligned_cols=54  Identities=17%  Similarity=0.233  Sum_probs=48.8

Q ss_pred             HHHHHHhhccCceEEEEEEecCCCCcceEEEEEecCHHHHHHHHHHhccCccCCceEEEEEc
Q psy3345          32 EQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKC   93 (787)
Q Consensus        32 ~~l~~~f~~~g~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~i~v~~~   93 (787)
                      .+|.+-|+.||+|.=|+++-+       -.+|+|.+-+.|-+|++. ++..+.|+.|.|..-
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~l-~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLDV-DGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHHG-GGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhcc-CCeEEcceEEEEecC
Confidence            468899999999999999875       899999999999999997 999999999999643

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.99  E-value=0.16  Score=39.24  Aligned_cols=58  Identities=21%  Similarity=0.358  Sum_probs=47.4

Q ss_pred             CCCCEEEEecCCccCcHHHHHHHHHhcCCeeEEEeccccCCCCCCceEEEEEecCHHHHHHHHHHhc
Q psy3345         683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC  749 (787)
Q Consensus       683 ~~~~~l~V~nLp~~~t~~dL~~~F~~~G~I~~v~i~~~~~~~g~~~g~afV~F~~~~~A~~Al~~l~  749 (787)
                      ....-||.-..|.+|...||.++|+.||.|.--.| -+   +     -|||...+.++|..++..++
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd---T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD---T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET---T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC---c-----eEEEEecCHHHHHHHHHHhc
Confidence            34456888889999999999999999998864444 33   1     69999999999999998764

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.92  E-value=0.1  Score=40.28  Aligned_cols=52  Identities=15%  Similarity=0.201  Sum_probs=47.7

Q ss_pred             eEEEeCCCCCCCHHhHHHhhcCCCCcceeecccceEEEeecChHhHHHHHhc
Q psy3345         226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNK  277 (787)
Q Consensus       226 ~v~v~nLp~~~te~di~~~F~~~g~v~i~i~~~g~afV~F~~~~~A~~Al~~  277 (787)
                      -|+.-..|......||.++|++||-+.|..+....|||...+.++|..++..
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIddTSa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCceEEEEecCceEEEEecCHHHHHHHHHH
Confidence            4888899999999999999999999999888778999999999999988873